Package ‘sangeranalyseR’

November 30, 2024

Type Package
Title sangeranalyseR: a suite of functions for the analysis of Sanger
sequence data in R
Version 1.17.0
Date 2024-04-24
Author Rob Lanfear <rob.lanfear@gmail.com>, Kuan-Hao Chao <ntueeb05howard@gmail.com>
Maintainer Kuan-Hao Chao <ntueeb05howard@gmail.com>
biocViews Genetics, Alignment, Sequencing, SangerSeq, Preprocessing,
QualityControl, Visualization, GUI
Description This package builds on sangerseqR to allow users to create contigs
from collections of Sanger sequencing reads. It provides a wide
range of options for a number of commonly-performed actions
including read trimming, detecting secondary peaks, and detecting
indels using a reference sequence. All parameters can be adjusted
interactively either in R or in the associated Shiny applications.
There is extensive online documentation, and the package can outputs
detailed HTML reports, including chromatograms.
License GPL-2
Encoding UTF-8
Depends R (>= 4.0.0), stringr, ape, Biostrings, pwalign, DECIPHER,
parallel, reshape2, sangerseqR, gridExtra, shiny,
shinydashboard, shinyjs, data.table, plotly, DT, zeallot,
excelR, shinycssloaders, ggdendro, shinyWidgets, openxlsx,
tools, rmarkdown (>= 2.9), knitr (>= 1.33), seqinr, BiocStyle,
logger
RoxygenNote 7.2.1
VignetteBuilder knitr
Suggests testthat (>= 2.1.0)
Collate 'AllGenerics.R' 'ClassChromatogramParam.R'
'ClassObjectResults.R' 'ClassQualityReport.R'
'ClassSangerRead.R' 'ClassSangerAlignment.R'
'ClassSangerContig.R' 'Constructors.R' 'LoadMessage.R'

1
2 Contents

'MethodSangerAlignment.R' 'MethodSangerContig.R'
'MethodSangerRead.R' 'MethodShared.R' 'MethodsQualityReport.R'
'ShinySangerAlignmentServer.R' 'ShinySangerAlignmentUI.R'
'ShinySangerContigServer.R' 'ShinySangerContigUI.R'
'ShinyServerModule.R' 'UtilitiesFunc.R'
'UtilitiesFuncInputChecker.R' 'data.R'
'sangeranalyseR_package.R' 'sangeranalyseR_show_method.R'
git_url https://git.bioconductor.org/packages/sangeranalyseR
git_branch devel
git_last_commit dca5e3f
git_last_commit_date 2024-10-29
Repository Bioconductor 3.21
Date/Publication 2024-11-29

Contents
ChromatogramParam-class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
generateReport . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
generateReportSA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
generateReportSC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
generateReportSR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
launchApp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
launchAppSA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
launchAppSC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
MakeBaseCalls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
ObjectResults-class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
qualityBasePlot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
QualityReport-class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
QualityReport-class-qualityBasePlot . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
QualityReport-class-updateQualityParam . . . . . . . . . . . . . . . . . . . . . . . . . 14
qualityReportData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
readTable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
SangerAlignment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
SangerAlignment-class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
SangerAlignment-class-generateReportSA . . . . . . . . . . . . . . . . . . . . . . . . . 22
SangerAlignment-class-launchAppSA . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
SangerAlignment-class-updateQualityParam . . . . . . . . . . . . . . . . . . . . . . . . 24
SangerAlignment-class-writeFastaSA . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
sangerAlignmentData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
sangeranalyseR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
SangerContig . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
SangerContig-class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
SangerContig-class-generateReportSC . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
SangerContig-class-launchAppSC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
SangerContig-class-readTable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
SangerContig-class-updateQualityParam . . . . . . . . . . . . . . . . . . . . . . . . . . 36
ChromatogramParam-class 3

SangerContig-class-writeFastaSC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
sangerContigData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
SangerRead . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
SangerRead-class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
SangerRead-class-generateReportSR . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
SangerRead-class-MakeBaseCalls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
SangerRead-class-qualityBasePlot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
SangerRead-class-readTable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
SangerRead-class-updateQualityParam . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
SangerRead-class-writeFastaSR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
sangerReadFData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
updateQualityParam . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
writeFasta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
writeFastaSA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
writeFastaSC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
writeFastaSR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

Index 54

ChromatogramParam-class
ChromatogramParam

Description
An S4 class storing chromatogram related inputs in a SangerRead S4 object.

Slots
baseNumPerRow It defines maximum base pairs in each row. The default value is 100.
heightPerRow It defines the height of each row in chromatogram. The default value is 200.
signalRatioCutoff The ratio of the height of a secondary peak to a primary peak. Secondary
peaks higher than this ratio are annotated. Those below the ratio are excluded. The default
value is 0.33.
showTrimmed The logical value storing whether to show trimmed base pairs in chromatogram. The
default value is TRUE.

Author(s)
Kuan-Hao Chao

Examples
Chromatogram <- new("ChromatogramParam",
baseNumPerRow = 100,
heightPerRow = 200,
signalRatioCutoff = 0.33,
showTrimmed = TRUE)
4 generateReport

generateReport Method generateReport

Description

A method which generates final reports of the SangerRead, SangerContig, and SangerAlignment
instance.

Usage

generateReport(
object,
outputDir = NULL,
includeSangerContig = TRUE,
includeSangerRead = TRUE,
colors = "default",
...
)

Arguments

object A SangerRead, SangerContig, or SangerAlignment S4 instance.

outputDir The output directory of the generated HTML report.
includeSangerContig
The parameter that decides whether to include SangerContig level report. The
value is TRUE or FALSE and the default is TRUE.
includeSangerRead
The parameter that decides whether to include SangerRead level report. The
value is TRUE or FALSE and the default is TRUE.
colors A vector for users to set the colors of (A, T, C, G, else). There are three options
for users to choose from. 1. "default": (green, blue, black, red, purple). 2.
"cb_friendly": ((0, 0, 0), (199, 199, 199), (0, 114, 178), (213, 94, 0), (204, 121,
167)). 3. Users can set their own colors with a vector with five elements.
... Further generateReportSR, generateReportSC, and generateReportSA related
parameters.

Value

A SangerRead, SangerContig, or SangerAlignment object.

Author(s)

Kuan-Hao Chao
generateReportSA 5

Examples
data(sangerReadFData)
data(sangerContigData)
data(sangerAlignmentData)
## Not run:
generateReport(sangerReadFData)
generateReport(sangerReadFData, colors="cb_friendly")
generateReport(sangerContigData)
generateReport(sangerContigData, colors="cb_friendly")
generateReport(sangerAlignmentData)
generateReport(sangerAlignmentData, colors="cb_friendly")
## End(Not run)

generateReportSA Method generateReportSA

Description
Method generateReportSA

Usage
generateReportSA(
object,
outputDir = NULL,
includeSangerContig = TRUE,
includeSangerRead = TRUE,
colors = "default",
...
)

Arguments
object A SangerAlignment S4 instance.
outputDir The output directory of the generated HTML report.
includeSangerContig
The parameter that decides whether to include SangerContig level report. The
value is TRUE or FALSE and the default is TRUE.
includeSangerRead
The parameter that decides whether to include SangerRead level report. The
value is TRUE or FALSE and the default is TRUE.
colors A vector for users to set the colors of (A, T, C, G, else). There are three options
for users to choose from. 1. "default": (green, blue, black, red, purple). 2.
"cb_friendly": ((0, 0, 0), (199, 199, 199), (0, 114, 178), (213, 94, 0), (204, 121,
167)). 3. Users can set their own colors with a vector with five elements.
... Further generateReportSA-related parameters.
6 generateReportSC

Value
The output absolute path to the SangerAlignment’s HTML file.

Examples
data(sangerAlignmentData)
## Not run:
generateReportSA(sangerAlignmentData)
## End(Not run)

generateReportSC Method generateReportSC

Description
Method generateReportSC

Usage
generateReportSC(
object,
outputDir = NULL,
includeSangerRead = TRUE,
colors = "default",
...
)

Arguments
object A SangerContig S4 instance.
outputDir The output directory of the generated HTML report.
includeSangerRead
The parameter that decides whether to include SangerRead level report. The
value is TRUE or FALSE and the default is TRUE.
colors A vector for users to set the colors of (A, T, C, G, else). There are three options
for users to choose from. 1. "default": (green, blue, black, red, purple). 2.
"cb_friendly": ((0, 0, 0), (199, 199, 199), (0, 114, 178), (213, 94, 0), (204, 121,
167)). 3. Users can set their own colors with a vector with five elements.
... Further generateReportSC-related parameters.

Value
The output absolute path to the SangerContig’s HTML file.
generateReportSR 7

Examples

data(sangerContigData)
## Not run:
generateReportSC(sangerContigData)
## End(Not run)

generateReportSR Method generateReportSR

Description

Method generateReportSR

Usage

generateReportSR(object, outputDir = NULL, colors = "default", ...)

Arguments

object A SangerRead S4 instance.

outputDir The output directory of the generated HTML report.
colors A vector for users to set the colors of (A, T, C, G, else). There are three options
for users to choose from. 1. "default": (green, blue, black, red, purple). 2.
"cb_friendly": ((0, 0, 0), (199, 199, 199), (0, 114, 178), (213, 94, 0), (204, 121,
167)). 3. Users can set their own colors with a vector with five elements.
... Further generateReportSR-related parameters.

Value

The output absolute path to the SangerRead’s HTML file.

Examples

data(sangerReadFData)
## Not run:
generateReportSR(sangerReadFData)
## End(Not run)
8 launchApp

launchApp Method launchApp

Description

A method which launches Shiny application of the SangerContig and SangerAlignment instance.

Usage

launchApp(object, outputDir = NULL, colors = "default")

Arguments

object A SangerContig or SangerAlignment S4 instance.

outputDir The output directory of the saved new SangerContig or SangerAlignment S4
instance.
colors A vector for users to set the colors of (A, T, C, G, else). There are three options
for users to choose from. 1. "default": (green, blue, black, red, purple). 2.
"cb_friendly": ((0, 0, 0), (199, 199, 199), (0, 114, 178), (213, 94, 0), (204, 121,
167)). 3. Users can set their own colors with a vector with five elements.

Value

A SangerContig or SangerAlignment object.

Author(s)

Kuan-Hao Chao

Examples

data(sangerContigData)
data(sangerAlignmentData)
## Not run:
launchApp(sangerContigData)
launchApp(sangerContigData, colors="cb_friendly")
launchApp(sangerAlignmentData)
launchApp(sangerAlignmentData, colors="cb_friendly")
## End(Not run)
launchAppSA 9

launchAppSA Method launchAppSA

Description
Method launchAppSA

Usage
launchAppSA(object, outputDir = NULL, colors = "default")

Arguments
object A SangerAlignment S4 instance.
outputDir The output directory of the saved new SangerAlignment S4 instance.
colors A vector for users to set the colors of (A, T, C, G, else). There are three options
for users to choose from. 1. "default": (green, blue, black, red, purple). 2.
"cb_friendly": ((0, 0, 0), (199, 199, 199), (0, 114, 178), (213, 94, 0), (204, 121,
167)). 3. Users can set their own colors with a vector with five elements.

Value
A shiny.appobj object.

Examples
data(sangerAlignmentData)
## Not run:
launchAppSA(sangerAlignmentData)
## End(Not run)

launchAppSC Method launchAppSC

Description
Method launchAppSC

Usage
launchAppSC(object, outputDir = NULL, colors = "default")
10 MakeBaseCalls

Arguments
object A SangerContig S4 instance.
outputDir The output directory of the saved new SangerContig S4 instance.
colors A vector for users to set the colors of (A, T, C, G, else). There are three options
for users to choose from. 1. "default": (green, blue, black, red, purple). 2.
"cb_friendly": ((0, 0, 0), (199, 199, 199), (0, 114, 178), (213, 94, 0), (204, 121,
167)). 3. Users can set their own colors with a vector with five elements.

Value
A shiny.appobj object.

Examples
data(sangerContigData)
## Not run:
launchAppSC(sangerContigData)
## End(Not run)

MakeBaseCalls Method MakeBaseCalls

Description
Method MakeBaseCalls

Usage
MakeBaseCalls(object, signalRatioCutoff = 0.33)

Arguments
object A SangerRead S4 instance.
signalRatioCutoff
The ratio of the height of a secondary peak to a primary peak. Secondary peaks
higher than this ratio are annotated. Those below the ratio are excluded. The
default value is 0.33.

Value
A SangerRead instance.

Examples
data(sangerReadFData)
MakeBaseCalls(sangerReadFData, signalRatioCutoff = 0.22)
ObjectResults-class 11

ObjectResults-class ObjectResults

Description
An S4 class storing results related inputs in a SangerRead, SangerContig, and SangerAlignment S4
object.

Slots
printLevel

Author(s)
Kuan-Hao Chao

Examples
objectResults <- new("ObjectResults",
creationResult = TRUE,
errorMessages = character(0),
errorTypes = character(0),
warningMessages = character(0),
warningTypes = character(0),
readResultTable = data.frame(),
printLevel = "SangerRead")

qualityBasePlot Method qualityBasePlot

Description
Method qualityBasePlot

Usage
qualityBasePlot(object)

Arguments
object A QualityReport or SangerRead S4 instance

Value
A quality plot.
12 QualityReport-class

Examples
data(qualityReportData)
data(sangerReadFData)
qualityBasePlot(qualityReportData)
qualityBasePlot(sangerReadFData)

QualityReport-class QualityReport

Description
An S4 class storing quality related inputs and results in a SangerRead S4 object.

Slots
TrimmingMethod The read trimming method for this SangerRead. The value must be "M1" (the
default) or 'M2'.
M1TrimmingCutoff The trimming cutoff for the Method 1. If TrimmingMethod is "M1", then the
default value is 0.0001. Otherwise, the value must be NULL.
M2CutoffQualityScore The trimming cutoff quality score for the Method 2. If TrimmingMethod
is 'M2', then the default value is 20. Otherwise, the value must be NULL. It works with
M2SlidingWindowSize.
M2SlidingWindowSize The trimming sliding window size for the Method 2. If TrimmingMethod
is 'M2', then the default value is 10. Otherwise, the value must be NULL. It works with
M2CutoffQualityScore.
qualityPhredScores The Phred quality scores of each base pairs after base calling.
qualityBaseScores The probability of incorrect base call of each base pairs. They are calculated
from qualityPhredScores.
rawSeqLength The number of nucleotides of raw primary DNA sequence.
trimmedSeqLength The number of nucleotides of trimeed primary DNA sequence.
trimmedStartPos The base pair index of trimming start point from 5’ end of the sequence.
trimmedFinishPos The base pair index of trimming finish point from 3’ end of the sequence.
rawMeanQualityScore The mean quality score of the primary sequence after base calling. In other
words, it is the mean of qualityPhredScores.
trimmedMeanQualityScore The mean quality score of the trimmed primary sequence after base
calling.
rawMinQualityScore The minimum quality score of the primary sequence after base calling.
trimmedMinQualityScore The minimum quality score of the trimmed primary sequence after
base calling.
remainingRatio The remaining sequence length ratio after trimming.

Author(s)
Kuan-Hao Chao
QualityReport-class-qualityBasePlot 13

Examples
inputFilesPath <- system.file("extdata/", package = "sangeranalyseR")
A_chloroticaFFN <- file.path(inputFilesPath,
"Allolobophora_chlorotica",
"ACHLO",
"Achl_ACHLO006-09_1_F.ab1")
sangerReadF <- new("SangerRead",
inputSource = "ABIF",
readFeature = "Forward Read",
readFileName = A_chloroticaFFN,
geneticCode = GENETIC_CODE,
TrimmingMethod = "M1",
M1TrimmingCutoff = 0.0001,
M2CutoffQualityScore = NULL,
M2SlidingWindowSize = NULL,
baseNumPerRow = 100,
heightPerRow = 200,
signalRatioCutoff = 0.33,
showTrimmed = TRUE)
"@"(sangerReadF, QualityReport)

QualityReport-class-qualityBasePlot
qualityBasePlot

Description
A QualityReport method which creates quality base interactive plot.

Usage
## S4 method for signature 'QualityReport'
qualityBasePlot(object)

Arguments
object A QualityReport S4 instance.

Value
A quality plot.

Examples
data("qualityReportData")
## Not run:
qualityBasePlot(qualityReportData)
## End(Not run)
14 QualityReport-class-updateQualityParam

QualityReport-class-updateQualityParam
updateQualityParam

Description
A QualityReport method which updates quality base interactive plot.

Usage
## S4 method for signature 'QualityReport'
updateQualityParam(
object,
TrimmingMethod = "M1",
M1TrimmingCutoff = 1e-04,
M2CutoffQualityScore = NULL,
M2SlidingWindowSize = NULL
)

Arguments
object A QualityReport S4 instance.
TrimmingMethod The read trimming method for this SangerRead. The value must be "M1" (the
default) or 'M2'.
M1TrimmingCutoff
The trimming cutoff for the Method 1. If TrimmingMethod is "M1", then the
default value is 0.0001. Otherwise, the value must be NULL.
M2CutoffQualityScore
The trimming cutoff quality score for the Method 2. If TrimmingMethod is 'M2',
then the default value is 20. Otherwise, the value must be NULL. It works with
M2SlidingWindowSize.
M2SlidingWindowSize
The trimming sliding window size for the Method 2. If TrimmingMethod is
'M2', then the default value is 10. Otherwise, the value must be NULL. It works
with M2CutoffQualityScore.

Value
A QualityReport instance.

Examples
data("qualityReportData")
updateQualityParam(qualityReportData,
TrimmingMethod = "M2",
M1TrimmingCutoff = NULL,
M2CutoffQualityScore = 30,
M2SlidingWindowSize = 15)
qualityReportData 15

qualityReportData QualityReport instance

Description
QualityReport instance

Usage
data(qualityReportData)

Author(s)
Kuan-Hao Chao

readTable Method readTable

Description
Method readTable

Usage
readTable(object, indentation = 0, ...)

Arguments
object A SangerRead, SangerContig, or SangerAlignment S4 instance.
indentation The indentation for different level printing
... Further generateReportSR-related parameters.

Value
None.

Examples
data(sangerReadFData)
data(sangerContigData)
data(sangerAlignmentData)
## Not run:
readTable(sangerReadFData)
readTable(sangerContigData)
readTable(sangerAlignmentData)

## End(Not run)
16 SangerAlignment

SangerAlignment SangerAlignment

Description
the wrapper function for SangerAlignment

Usage
SangerAlignment(
printLevel = "SangerAlignment",
inputSource = "ABIF",
processMethod = "REGEX",
ABIF_Directory = NULL,
FASTA_File = NULL,
REGEX_SuffixForward = NULL,
REGEX_SuffixReverse = NULL,
CSV_NamesConversion = NULL,
geneticCode = GENETIC_CODE,
TrimmingMethod = "M1",
M1TrimmingCutoff = 1e-04,
M2CutoffQualityScore = NULL,
M2SlidingWindowSize = NULL,
baseNumPerRow = 100,
heightPerRow = 200,
signalRatioCutoff = 0.33,
showTrimmed = TRUE,
refAminoAcidSeq = "",
minReadsNum = 2,
minReadLength = 20,
minFractionCall = 0.5,
maxFractionLost = 0.5,
acceptStopCodons = TRUE,
readingFrame = 1,
processorsNum = 1
)

Arguments
inputSource The input source of the raw file. It must be "ABIF" or "FASTA". The default
value is "ABIF".
ABIF_Directory The parent directory of all of the reads contained in ABIF format you wish to
analyse. In SangerAlignment, all reads in subdirectories will be scanned recur-
sively.
FASTA_File If inputSource is "FASTA", then this value has to be the name of the FASTA
file; if inputSource is "ABIF", then this value is "" by default.
SangerAlignment 17

REGEX_SuffixForward
The suffix of the filenames for forward reads in regular expression, i.e. reads
that do not need to be reverse-complemented. For forward reads, it should be
"_F.ab1".
REGEX_SuffixReverse
The suffix of the filenames for reverse reads in regular expression, i.e. reads that
need to be reverse-complemented. For revcerse reads, it should be "_R.ab1".
CSV_NamesConversion
The file path to the CSV file that provides read names that follow the naming
regulation. If inputSource is "FASTA", then users need to prepare the csv file
or make sure the original names inside FASTA file are valid; if inputSource is
"ABIF", then this value is NULL by default.
geneticCode Named character vector in the same format as GENETIC_CODE (the default),
which represents the standard genetic code. This is the code with which the
function will attempt to translate your DNA sequences. You can get an appro-
priate vector with the getGeneticCode() function. The default is the standard
code.
TrimmingMethod TrimmingMethod The read trimming method for this SangerRead. The value
must be "M1" (the default) or 'M2'.
M1TrimmingCutoff
The trimming cutoff for the Method 1. If TrimmingMethod is "M1", then the
default value is 0.0001. Otherwise, the value must be NULL.
M2CutoffQualityScore
The trimming cutoff quality score for the Method 2. If TrimmingMethod is 'M2',
then the default value is 20. Otherwise, the value must be NULL. It works with
M2SlidingWindowSize.
M2SlidingWindowSize
The trimming sliding window size for the Method 2. If TrimmingMethod is
'M2', then the default value is 10. Otherwise, the value must be NULL. It works
with M2CutoffQualityScore.
baseNumPerRow It defines maximum base pairs in each row. The default value is 100.
heightPerRow It defines the height of each row in chromatogram. The default value is 200.
signalRatioCutoff
The ratio of the height of a secondary peak to a primary peak. Secondary peaks
higher than this ratio are annotated. Those below the ratio are excluded. The
default value is 0.33.
showTrimmed The logical value storing whether to show trimmed base pairs in chromatogram.
The default value is TRUE.
refAminoAcidSeq
An amino acid reference sequence supplied as a string or an AAString object.
If your sequences are protein-coding DNA seuqences, and you want to have
frameshifts automatically detected and corrected, supply a reference amino acid
sequence via this argument. If this argument is supplied, the sequences are then
kept in frame for the alignment step. Fwd sequences are assumed to come from
the sense (i.e. coding, or "+") strand. The default value is "".
18 SangerAlignment

minReadsNum The minimum number of reads required to make a consensus sequence, must be
2 or more. The default value is 2.
minReadLength Reads shorter than this will not be included in the readset. The default 20 means
that all reads with length of 20 or more will be included. Note that this is the
length of a read after it has been trimmed.
minFractionCall
Minimum fraction of the sequences required to call a consensus sequence for
SangerContig at any given position (see the ConsensusSequence() function from
DECIPHER for more information). Defaults to 0.75 implying that 3/4 of all
reads must be present in order to call a consensus.
maxFractionLost
Numeric giving the maximum fraction of sequence information that can be
lost in the consensus sequence for SangerContig (see the ConsensusSequence()
function from DECIPHER for more information). Defaults to 0.5, implying that
each consensus base can ignore at most 50 percent of the information at a given
position.
acceptStopCodons
The logical value TRUE or FALSE. TRUE (the defualt): keep all reads, regardless of
whether they have stop codons; FALSE: reject reads with stop codons. If FALSE is
selected, then the number of stop codons is calculated after attempting to correct
frameshift mutations (if applicable).
readingFrame 1, 2, or 3. Only used if accept.stop.codons == FALSE. This specifies the read-
ing frame that is used to determine stop codons. If you use a refAminoAcidSeq,
then the frame should always be 1, since all reads will be shifted to frame 1 dur-
ing frameshift correction. Otherwise, you should select the appropriate reading
frame.
processorsNum The number of processors to use, or NULL (the default) for all available proces-
sors.
minFractionCallSA
Minimum fraction of the sequences required to call a consensus sequence for
SangerAlignment at any given position (see the ConsensusSequence() function
from DECIPHER for more information). Defaults to 0.75 implying that 3/4 of
all reads must be present in order to call a consensus.
maxFractionLostSA
Numeric giving the maximum fraction of sequence information that can be lost
in the consensus sequence for SangerAlignment (see the ConsensusSequence()
function from DECIPHER for more information). Defaults to 0.5, implying that
each consensus base can ignore at most 50 percent of the information at a given
position.

Value
A SangerAlignment instance.

Author(s)
Kuan-Hao Chao
SangerAlignment-class 19

Examples
rawDataDir <- system.file("extdata", package = "sangeranalyseR")
parentDir <- file.path(rawDataDir, "Allolobophora_chlorotica", "RBNII")
REGEX_SuffixForward <- "_[0-9]*_F.ab1$"
REGEX_SuffixReverse <- "_[0-9]*_R.ab1$"
sangerAlignment <- SangerAlignment(
inputSource = "ABIF",
ABIF_Directory = parentDir,
REGEX_SuffixForward = REGEX_SuffixForward,
REGEX_SuffixReverse = REGEX_SuffixReverse,
refAminoAcidSeq = "SRQWLFSTNHKDIGTLYFIFGAWAGMVGTSLSILIRAELGHPGALIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFG
TrimmingMethod = "M1",
M1TrimmingCutoff = 0.0001,
M2CutoffQualityScore = NULL,
M2SlidingWindowSize = NULL,
baseNumPerRow = 100,
heightPerRow = 200,
signalRatioCutoff = 0.33,
showTrimmed = TRUE,
processorsNum = 2)

SangerAlignment-class SangerAlignment

Description
An S4 class containing SangerContigs lists and contigs alignment results which corresponds to a
final alignment in Sanger sequencing.

Slots
objectResults This is the object that stores all information of the creation result.
inputSource The input source of the raw file. It must be "ABIF" or "FASTA". The default value is
"ABIF".
processMethod The method to create a contig from reads. The value is "REGEX" or "CSV". The
default value is "REGEX".
ABIF_Directory If inputSource is "ABIF", then this value is the path of a parent directory storing
all reads in ABIF format you want to analyse. If inputSource is "FASTA", then this value has
to be NULL by default.
FASTA_File If inputSource is "FASTA", then this value has to be the path to a valid FASTA file ;
if inputSource is "ABIF", then this value has to be NULL by default.
REGEX_SuffixForward The suffix of the filenames for forward reads in regular expression, i.e.
reads that do not need to be reverse-complemented. For forward reads, it should be "_F.ab1".
REGEX_SuffixReverse The suffix of the filenames for reverse reads in regular expression, i.e.
reads that need to be reverse-complemented. For revcerse reads, it should be "_R.ab1".
20 SangerAlignment-class

CSV_NamesConversion The file path to the CSV file that provides read names, directions, and their
contig groups. If processMethod is "CSV", then this value has to be the path to a valid CSV
file; if processMethod is "REGEX", then this value has to be NULL by default.
geneticCode Named character vector in the same format as GENETIC_CODE (the default), which
represents the standard genetic code. This is the code with which the function will attempt to
translate your DNA sequences. You can get an appropriate vector with the getGeneticCode()
function. The default is the standard code.
refAminoAcidSeq An amino acid reference sequence supplied as a string or an AAString object.
If your sequences are protein-coding DNA seuqences, and you want to have frameshifts auto-
matically detected and corrected, supply a reference amino acid sequence via this argument.
If this argument is supplied, the sequences are then kept in frame for the alignment step. Fwd
sequences are assumed to come from the sense (i.e. coding, or "+") strand. The default value
is "".
contigList A list storing all SangerContigs S4 instances.
contigsConsensus The consensus read of all SangerContig S4 instances in DNAString object.
contigsAlignment The alignment of all SangerContig S4 instances with the called consensus
sequence in DNAStringSet object. Users can use BrowseSeqs() to view the alignment.
contigsTree A phylo instance returned by bionj function in ape package. It can be used to draw
the tree.

Author(s)
Kuan-Hao Chao

Examples
## Simple example
rawDataDir <- system.file("extdata", package = "sangeranalyseR")
parentDir <- file.path(rawDataDir, 'Allolobophora_chlorotica', 'ACHLO')
my_aligned_contigs <- new("SangerAlignment",
ABIF_Directory = parentDir,
REGEX_SuffixForward = "_[0-9]*_F.ab1$",
REGEX_SuffixReverse = "_[0-9]*_R.ab1$")

rawDataDir <- system.file("extdata", package = "sangeranalyseR")

parentDir <- file.path(rawDataDir, 'Allolobophora_chlorotica', 'ACHLO')
CSV_NamesConversion <- file.path(rawDataDir, "ab1", "SangerAlignment", "names_conversion.csv")
sangerAlignment <- new("SangerAlignment",
processMethod = "CSV",
ABIF_Directory = parentDir,
CSV_NamesConversion = CSV_NamesConversion)

## Input From ABIF file format (Regex)

REGEX_SuffixForward <- "_[0-9]*_F.ab1$"
REGEX_SuffixReverse <- "_[0-9]*_R.ab1$"
sangerAlignment <- new("SangerAlignment",
printLevel = "SangerAlignment",
inputSource = "ABIF",
processMethod = "REGEX",
SangerAlignment-class 21

FASTA_File = NULL,
CSV_NamesConversion = NULL,
ABIF_Directory = parentDir,
REGEX_SuffixForward = REGEX_SuffixForward,
REGEX_SuffixReverse = REGEX_SuffixReverse,
TrimmingMethod = "M1",
M1TrimmingCutoff = 0.0001,
M2CutoffQualityScore = NULL,
M2SlidingWindowSize = NULL,
baseNumPerRow = 100,
heightPerRow = 200,
signalRatioCutoff = 0.33,
showTrimmed = TRUE,
refAminoAcidSeq = "SRQWLFSTNHKDIGTLYFIFGAWAGMVGTSLSILIRAELGHPGALIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFG
minReadsNum = 2,
minReadLength = 20,
minFractionCall = 0.5,
maxFractionLost = 0.5,
geneticCode = GENETIC_CODE,
acceptStopCodons = TRUE,
readingFrame = 1,
processorsNum = 2)

## Input From ABIF file format (Csv three column)

rawDataDir <- system.file("extdata", package = "sangeranalyseR")
parentDir <- file.path(rawDataDir, 'Allolobophora_chlorotica', 'ACHLO')
CSV_NamesConversion <- file.path(rawDataDir, "ab1", "SangerAlignment",
"names_conversion_all.csv")
sangerAlignment <- new("SangerAlignment",
inputSource = "ABIF",
processMethod = "CSV",
ABIF_Directory = parentDir,
CSV_NamesConversion = CSV_NamesConversion,
refAminoAcidSeq = "SRQWLFSTNHKDIGTLYFIFGAWAGMVGTSLSILIRAELGHPGALIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFG
TrimmingMethod = "M1",
M1TrimmingCutoff = 0.0001,
M2CutoffQualityScore = NULL,
M2SlidingWindowSize = NULL,
baseNumPerRow = 100,
heightPerRow = 200,
signalRatioCutoff = 0.33,
showTrimmed = TRUE,
processorsNum = 2)

## Input From FASTA file format (No Csv - Regex)

rawDataDir <- system.file("extdata", package = "sangeranalyseR")
fastaFN <- file.path(rawDataDir, "fasta",
"SangerAlignment", "Sanger_all_reads.fa")
REGEX_SuffixForwardFa <- "_[0-9]*_F$"
REGEX_SuffixReverseFa <- "_[0-9]*_R$"
sangerAlignmentFa <- new("SangerAlignment",
inputSource = "FASTA",
processMethod = "REGEX",
22 SangerAlignment-class-generateReportSA

FASTA_File = fastaFN,
REGEX_SuffixForward = REGEX_SuffixForwardFa,
REGEX_SuffixReverse = REGEX_SuffixReverseFa,
refAminoAcidSeq = "SRQWLFSTNHKDIGTLYFIFGAWAGMVGTSLSILIRAELGHPGALIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGF
processorsNum = 2)

## Input From FASTA file format (Csv three column method)

rawDataDir <- system.file("extdata", package = "sangeranalyseR")
fastaFN <- file.path(rawDataDir, "fasta",
"SangerAlignment", "Sanger_all_reads.fa")
CSV_NamesConversion <- file.path(rawDataDir, "fasta",
"SangerAlignment", "names_conversion.csv")
sangerAlignmentFa <- new("SangerAlignment",
inputSource = "FASTA",
processMethod = "CSV",
FASTA_File = fastaFN,
CSV_NamesConversion = CSV_NamesConversion,
refAminoAcidSeq = "SRQWLFSTNHKDIGTLYFIFGAWAGMVGTSLSILIRAELGHPGALIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGF
processorsNum = 2)

SangerAlignment-class-generateReportSA
generateReportSA

Description
A SangerAlignment method which generates final reports of the SangerContig instance.

Usage
## S4 method for signature 'SangerAlignment'
generateReportSA(
object,
outputDir,
includeSangerContig = TRUE,
includeSangerRead = TRUE,
colors
)

Arguments
object A SangerAlignment S4 instance.
outputDir The output directory of the generated HTML report.
includeSangerContig
The parameter that decides whether to include SangerContig level report. The
value is TRUE or FALSE and the default is TRUE.
includeSangerRead
The parameter that decides whether to include SangerRead level report. The
value is TRUE or FALSE and the default is TRUE.
SangerAlignment-class-launchAppSA 23

colors A vector for users to set the colors of (A, T, C, G, else). There are three options
for users to choose from. 1. "default": (green, blue, black, red, purple). 2.
"cb_friendly": ((0, 0, 0), (199, 199, 199), (0, 114, 178), (213, 94, 0), (204, 121,
167)). 3. Users can set their own colors with a vector with five elements.

Value
The output absolute path to the SangerAlignment’s HTML file.

Examples
data("sangerAlignmentData")
## Not run:
generateReportSA(sangerAlignmentData)
generateReportSA(sangerAlignmentData, colors="cb_friendly")
## End(Not run)

SangerAlignment-class-launchAppSA
launchAppSA

Description
A SangerAlignment method which launches Shiny app for SangerAlignment instance.

Usage
## S4 method for signature 'SangerAlignment'
launchAppSA(object, outputDir = NULL, colors = "default")

Arguments
object A SangerAlignment S4 instance.
outputDir The output directory of the saved new SangerContig S4 instance.
colors A vector for users to set the colors of (A, T, C, G, else). There are three options
for users to choose from. 1. "default": (green, blue, black, red, purple). 2.
"cb_friendly": ((0, 0, 0), (199, 199, 199), (0, 114, 178), (213, 94, 0), (204, 121,
167)). 3. Users can set their own colors with a vector with five elements.

Value
A shiny.appobj object.

Examples
data("sangerAlignmentData")
RShinySA <- launchAppSA(sangerAlignmentData)
RShinySA <- launchAppSA(sangerAlignmentData, colors="cb_friendly")
24 SangerAlignment-class-updateQualityParam

SangerAlignment-class-updateQualityParam
updateQualityParam

Description

A SangerAlignment method which updates QualityReport parameter for each the SangerRead in-
stance inside SangerAlignment.

Usage

## S4 method for signature 'SangerAlignment'

updateQualityParam(
object,
TrimmingMethod = "M1",
M1TrimmingCutoff = 1e-04,
M2CutoffQualityScore = NULL,
M2SlidingWindowSize = NULL,
processorsNum = NULL
)

Arguments

object A SangerAlignment S4 instance.

TrimmingMethod The read trimming method for this SangerRead. The value must be "M1" (the
default) or 'M2'.
M1TrimmingCutoff
The trimming cutoff for the Method 1. If TrimmingMethod is "M1", then the
default value is 0.0001. Otherwise, the value must be NULL.
M2CutoffQualityScore
The trimming cutoff quality score for the Method 2. If TrimmingMethod is 'M2',
then the default value is 20. Otherwise, the value must be NULL. It works with
M2SlidingWindowSize.
M2SlidingWindowSize
The trimming sliding window size for the Method 2. If TrimmingMethod is
'M2', then the default value is 10. Otherwise, the value must be NULL. It works
with M2CutoffQualityScore.
processorsNum The number of processors to use, or NULL (the default) for all available proces-
sors.

Value

A SangerAlignment instance.
SangerAlignment-class-writeFastaSA 25

Examples
data("sangerAlignmentData")
## Not run:
updateQualityParam(sangerAlignmentData,
TrimmingMethod = "M2",
M1TrimmingCutoff = NULL,
M2CutoffQualityScore = 40,
M2SlidingWindowSize = 15)
## End(Not run)

SangerAlignment-class-writeFastaSA
writeFastaSA

Description
A SangerAlignment method which writes sequences into Fasta files.

Usage
## S4 method for signature 'SangerAlignment'
writeFastaSA(
object,
outputDir = NULL,
compress = FALSE,
compression_level = NA,
selection = "all"
)

Arguments
object A SangerAlignment S4 instance.
outputDir The output directory of generated FASTA files.
compress Like for the save function in base R, must be TRUE or FALSE (the default), or a
single string specifying whether writing to the file is to use compression. The
only type of compression supported at the moment is "gzip". This parameter
will be passed to writeXStringSet function in Biostrings package.
compression_level
This parameter will be passed to writeXStringSet function in Biostrings pack-
age.
selection This value can be all, contigs_alignment, contigs_unalignment or all_reads.
It generates reads and contigs FASTA files.

Value
The output directory of FASTA files.
26 SangerContig

Examples

data("sangerAlignmentData")
writeFastaSA(sangerAlignmentData)

sangerAlignmentData SangerAlignment instance

Description

SangerAlignment instance

Usage

data(sangerAlignmentData)

Author(s)

Kuan-Hao Chao

sangeranalyseR sangeranalyseR-package

Description

sangeranalyseR-package

SangerContig SangerContig

Description

the wrapper function for SangerContig

SangerContig 27

Usage
SangerContig(
printLevel = "SangerContig",
inputSource = "ABIF",
processMethod = "REGEX",
ABIF_Directory = NULL,
FASTA_File = NULL,
REGEX_SuffixForward = NULL,
REGEX_SuffixReverse = NULL,
CSV_NamesConversion = NULL,
contigName = NULL,
geneticCode = GENETIC_CODE,
TrimmingMethod = "M1",
M1TrimmingCutoff = 1e-04,
M2CutoffQualityScore = NULL,
M2SlidingWindowSize = NULL,
baseNumPerRow = 100,
heightPerRow = 200,
signalRatioCutoff = 0.33,
showTrimmed = TRUE,
refAminoAcidSeq = "",
minReadsNum = 2,
minReadLength = 20,
minFractionCall = 0.5,
maxFractionLost = 0.5,
acceptStopCodons = TRUE,
readingFrame = 1,
processorsNum = 1
)

Arguments
inputSource The input source of the raw file. It must be "ABIF" or "FASTA". The default
value is "ABIF".
ABIF_Directory The parent directory of all of the reads contained in ABIF format you wish to
analyse. In SangerContig, all reads must be in the first layer in this directory.
FASTA_File If inputSource is "FASTA", then this value has to be the name of the FASTA
file; if inputSource is "ABIF", then this value is "" by default.
REGEX_SuffixForward
The suffix of the filenames for forward reads in regular expression, i.e. reads
that do not need to be reverse-complemented. For forward reads, it should be
"_F.ab1".
REGEX_SuffixReverse
The suffix of the filenames for reverse reads in regular expression, i.e. reads that
need to be reverse-complemented. For revcerse reads, it should be "_R.ab1".
CSV_NamesConversion
The file path to the CSV file that provides read names that follow the naming
regulation. If inputSource is "FASTA", then users need to prepare the csv file
28 SangerContig

or make sure the original names inside FASTA file are valid; if inputSource is
"ABIF", then this value is NULL by default.
contigName The contig name of all the reads in ABIF_Directory.
geneticCode Named character vector in the same format as GENETIC_CODE (the default),
which represents the standard genetic code. This is the code with which the
function will attempt to translate your DNA sequences. You can get an appro-
priate vector with the getGeneticCode() function. The default is the standard
code.
TrimmingMethod TrimmingMethod The read trimming method for this SangerRead. The value
must be "M1" (the default) or 'M2'.
M1TrimmingCutoff
The trimming cutoff for the Method 1. If TrimmingMethod is "M1", then the
default value is 0.0001. Otherwise, the value must be NULL.
M2CutoffQualityScore
The trimming cutoff quality score for the Method 2. If TrimmingMethod is 'M2',
then the default value is 20. Otherwise, the value must be NULL. It works with
M2SlidingWindowSize.
M2SlidingWindowSize
The trimming sliding window size for the Method 2. If TrimmingMethod is
'M2', then the default value is 10. Otherwise, the value must be NULL. It works
with M2CutoffQualityScore.
baseNumPerRow It defines maximum base pairs in each row. The default value is 100.
heightPerRow It defines the height of each row in chromatogram. The default value is 200.
signalRatioCutoff
The ratio of the height of a secondary peak to a primary peak. Secondary peaks
higher than this ratio are annotated. Those below the ratio are excluded. The
default value is 0.33.
showTrimmed The logical value storing whether to show trimmed base pairs in chromatogram.
The default value is TRUE.
refAminoAcidSeq
An amino acid reference sequence supplied as a string or an AAString object.
If your sequences are protein-coding DNA seuqences, and you want to have
frameshifts automatically detected and corrected, supply a reference amino acid
sequence via this argument. If this argument is supplied, the sequences are then
kept in frame for the alignment step. Fwd sequences are assumed to come from
the sense (i.e. coding, or "+") strand. The default value is "".
minReadsNum The minimum number of reads required to make a consensus sequence, must be
2 or more. The default value is 2.
minReadLength Reads shorter than this will not be included in the readset. The default 20 means
that all reads with length of 20 or more will be included. Note that this is the
length of a read after it has been trimmed.
minFractionCall
Minimum fraction of the sequences required to call a consensus sequence for
SangerContig at any given position (see the ConsensusSequence() function from
DECIPHER for more information). Defaults to 0.75 implying that 3/4 of all
reads must be present in order to call a consensus.
SangerContig 29

maxFractionLost
Numeric giving the maximum fraction of sequence information that can be
lost in the consensus sequence for SangerContig (see the ConsensusSequence()
function from DECIPHER for more information). Defaults to 0.5, implying that
each consensus base can ignore at most 50 percent of the information at a given
position.
acceptStopCodons
The logical value TRUE or FALSE. TRUE (the defualt): keep all reads, regardless of
whether they have stop codons; FALSE: reject reads with stop codons. If FALSE is
selected, then the number of stop codons is calculated after attempting to correct
frameshift mutations (if applicable).
readingFrame 1, 2, or 3. Only used if accept.stop.codons == FALSE. This specifies the read-
ing frame that is used to determine stop codons. If you use a refAminoAcidSeq,
then the frame should always be 1, since all reads will be shifted to frame 1 dur-
ing frameshift correction. Otherwise, you should select the appropriate reading
frame.
processorsNum The number of processors to use, or NULL (the default) for all available proces-
sors.

Value
A SangerContig instance.

Author(s)
Kuan-Hao Chao

Examples
rawDataDir <- system.file("extdata", package = "sangeranalyseR")
parentDir <- file.path(rawDataDir, "Allolobophora_chlorotica", "ACHLO")
contigName <- "Achl_ACHLO006-09"
REGEX_SuffixForward <- "_F.ab1"
REGEX_SuffixReverse <- "_R.ab1"
sangerContig <- SangerContig(
inputSource = "ABIF",
ABIF_Directory = parentDir,
contigName = contigName,
REGEX_SuffixForward = REGEX_SuffixForward,
REGEX_SuffixReverse = REGEX_SuffixReverse,
refAminoAcidSeq = "SRQWLFSTNHKDIGTLYFIFGAWAGMVGTSLSILIRAELGHPGALIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGN
TrimmingMethod = "M2",
M1TrimmingCutoff = NULL,
M2CutoffQualityScore = 20,
M2SlidingWindowSize = 10,
baseNumPerRow = 100,
heightPerRow = 200,
signalRatioCutoff = 0.33,
showTrimmed = TRUE,
processorsNum = 2)
30 SangerContig-class

SangerContig-class SangerContig

Description
An S4 class containing forward and reverse SangerRead lists and alignment, consensus read results
which corresponds to a contig in Sanger sequencing.

Slots
objectResults This is the object that stores all information of the creation result.
inputSource The input source of the raw file. It must be "ABIF" or "FASTA". The default value is
"ABIF".
processMethod The method to create a contig from reads. The value is "REGEX" or "CSV". The
default value is "REGEX".
ABIF_Directory If inputSource is "ABIF", then this value is the path of a parent directory storing
all reads in ABIF format you want to analyse. If inputSource is "FASTA", then this value has
to be NULL by default.
FASTA_File If inputSource is "FASTA", then this value has to be the path to a valid FASTA file ;
if inputSource is "ABIF", then this value has to be NULL by default.
REGEX_SuffixForward The suffix of the filenames for forward reads in regular expression, i.e.
reads that do not need to be reverse-complemented.
REGEX_SuffixReverse The suffix of the filenames for reverse reads in regular expression, i.e.
reads that need to be reverse-complemented.
CSV_NamesConversion The file path to the CSV file that provides read names, directions, and their
contig groups. If processMethod is "CSV", then this value has to be the path to a valid CSV
file; if processMethod is "REGEX", then this value has to be NULL by default.
contigName The contig name of all the reads in ABIF_Directory.
geneticCode Named character vector in the same format as GENETIC_CODE (the default), which
represents the standard genetic code. This is the code with which the function will attempt to
translate your DNA sequences. You can get an appropriate vector with the getGeneticCode()
function. The default is the standard code.
forwardReadList The list of SangerRead S4 instances which are all forward reads.
reverseReadList The list of SangerRead S4 instances which are all reverse reads.
minReadsNum The minimum number of reads required to make a consensus sequence, must be 2 or
more. The default value is 2.
minReadLength Reads shorter than this will not be included in the readset. The default 20 means
that all reads with length of 20 or more will be included. Note that this is the length of a read
after it has been trimmed.
refAminoAcidSeq An amino acid reference sequence supplied as a string or an AAString object.
If your sequences are protein-coding DNA seuqences, and you want to have frameshifts auto-
matically detected and corrected, supply a reference amino acid sequence via this argument.
SangerContig-class 31

If this argument is supplied, the sequences are then kept in frame for the alignment step. Fwd
sequences are assumed to come from the sense (i.e. coding, or "+") strand. The default value
is "".
minFractionCall Minimum fraction of the sequences required to call a consensus sequence for
SangerContig at any given position (see the ConsensusSequence() function from DECIPHER
for more information). Defaults to 0.75 implying that 3/4 of all reads must be present in order
to call a consensus.
maxFractionLost Numeric giving the maximum fraction of sequence information that can be lost
in the consensus sequence for SangerContig (see the ConsensusSequence() function from DE-
CIPHER for more information). Defaults to 0.5, implying that each consensus base can ignore
at most 50 percent of the information at a given position.
acceptStopCodons The logical value TRUE or FALSE. TRUE (the defualt): keep all reads, regardless
of whether they have stop codons; FALSE: reject reads with stop codons. If FALSE is selected,
then the number of stop codons is calculated after attempting to correct frameshift mutations
(if applicable).
readingFrame 1, 2, or 3. Only used if accept.stop.codons == FALSE. This specifies the reading
frame that is used to determine stop codons. If you use a refAminoAcidSeq, then the frame
should always be 1, since all reads will be shifted to frame 1 during frameshift correction.
Otherwise, you should select the appropriate reading frame.
contigSeq The consensus read of all SangerRead S4 instances in DNAString object.
alignment The alignment of all SangerRead S4 instances with the called consensus sequence in
DNAStringSet object. Users can use BrowseSeqs() to view the alignment.
differencesDF A data frame of the number of pairwise differences between each read and the
consensus sequence, as well as the number of bases in each input read that did not contribute
to the consensus sequence. It can assist in detecting incorrect reads, or reads with a lot of
errors.
distanceMatrix A distance matrix of genetic distances (corrected with the JC model) between all
of the input reads.
dendrogram A list storing cluster groups in a data frame and a dendrogram object depicting the
distance.matrix. Users can use plot() to see the dendrogram.
indelsDF If users specified a reference sequence via refAminoAcidSeq, then this will be a data
frame describing the number of indels and deletions that were made to each of the input reads
in order to correct frameshift mutations.
stopCodonsDF If users specified a reference sequence via refAminoAcidSeq, then this will be a
data frame describing the number of stop codons in each read.
secondaryPeakDF A data frame with one row for each column in the alignment that contained
more than one secondary peak. The data frame has three columns: the column number of
the alignment; the number of secondary peaks in that column; and the bases (with IUPAC
ambiguity codes representing secondary peak calls) in that column represented as a string.

Author(s)

Kuan-Hao Chao
32 SangerContig-class

Examples

## Simple example
rawDataDir <- system.file("extdata", package = "sangeranalyseR")
parentDir <- file.path(rawDataDir, "Allolobophora_chlorotica", "RBNII")
contigName <- "Achl_RBNII384-13"
REGEX_SuffixForward <- "_[0-9]*_F.ab1$"
REGEX_SuffixReverse <- "_[0-9]*_R.ab1$"
sangerContig <- new("SangerContig",
ABIF_Directory = parentDir,
contigName = contigName,
REGEX_SuffixForward = REGEX_SuffixForward,
REGEX_SuffixReverse = REGEX_SuffixReverse)

## forward / reverse reads match error

## Input From ABIF file format (Regex)
rawDataDir <- system.file("extdata", package = "sangeranalyseR")
parentDir <- file.path(rawDataDir, "Allolobophora_chlorotica", "ACHLO")
contigName <- "Achl_ACHLO006-09"
REGEX_SuffixForward <- "_[0-9]*_F.ab1$"
REGEX_SuffixReverse <- "_[0-9]*_R.ab1$"
sangerContig <- new("SangerContig",
inputSource = "ABIF",
processMethod = "REGEX",
ABIF_Directory = parentDir,
contigName = contigName,
REGEX_SuffixForward = REGEX_SuffixForward,
REGEX_SuffixReverse = REGEX_SuffixReverse,
refAminoAcidSeq = "SRQWLFSTNHKDIGTLYFIFGAWAGMVGTSLSILIRAELGHPGALIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGN
TrimmingMethod = "M1",
M1TrimmingCutoff = 0.0001,
baseNumPerRow = 100,
heightPerRow = 200,
signalRatioCutoff = 0.33,
showTrimmed = TRUE,
minReadsNum = 2,
processorsNum = 2)

## Input From ABIF file format (Csv three column method)

rawDataDir <- system.file("extdata", package = "sangeranalyseR")
parentDir <- file.path(rawDataDir, "Allolobophora_chlorotica", "RBNII")
CSV_NamesConversion <- file.path(rawDataDir, "ab1", "SangerContig", "names_conversion_2.csv")
sangerContig <- new("SangerContig",
inputSource = "ABIF",
processMethod = "CSV",
ABIF_Directory = parentDir,
CSV_NamesConversion = CSV_NamesConversion,
contigName = "Achl_RBNII384-13",
refAminoAcidSeq = "SRQWLFSTNHKDIGTLYFIFGAWAGMVGTSLSILIRAELGHPGALIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGN
TrimmingMethod = "M1",
M1TrimmingCutoff = 0.000001,
baseNumPerRow = 100,
heightPerRow = 200,
SangerContig-class-generateReportSC 33

signalRatioCutoff = 0.33,
showTrimmed = TRUE,
processorsNum = 2)

## Input From FASTA file format (Regex)

rawDataDir <- system.file("extdata", package = "sangeranalyseR")
fastaFN <- file.path(rawDataDir, "fasta",
"SangerContig", "Achl_ACHLO006-09.fa")
contigName <- "Achl_ACHLO006-09"
REGEX_SuffixForwardFa <- "_[0-9]*_F$"
REGEX_SuffixReverseFa <- "_[0-9]*_R$"
sangerContigFa <- new("SangerContig",
inputSource = "FASTA",
processMethod = "REGEX",
FASTA_File = fastaFN,
contigName = contigName,
REGEX_SuffixForward = REGEX_SuffixForwardFa,
REGEX_SuffixReverse = REGEX_SuffixReverseFa,
refAminoAcidSeq = "SRQWLFSTNHKDIGTLYFIFGAWAGMVGTSLSILIRAELGHPGALIGDDQIYNVIVTAHAFIMIFFMVMPIMIG
processorsNum = 2)

## Input From FASTA file format (Csv - Csv three column method)
rawDataDir <- system.file("extdata", package = "sangeranalyseR")
fastaFN <- file.path(rawDataDir, "fasta",
"SangerContig", "Achl_ACHLO006-09.fa")
CSV_NamesConversion <- file.path(rawDataDir, "fasta", "SangerContig", "names_conversion_1.csv")
sangerContigFa <- new("SangerContig",
inputSource = "FASTA",
processMethod = "CSV",
FASTA_File = fastaFN,
CSV_NamesConversion = CSV_NamesConversion,
contigName = "Achl_ACHLO006-09",
refAminoAcidSeq = "SRQWLFSTNHKDIGTLYFIFGAWAGMVGTSLSILIRAELGHPGALIGDDQIYNVIVTAHAFIMIFFMVMPIMIG
processorsNum = 2)

SangerContig-class-generateReportSC
generateReportSC

Description
A SangerContig method which generates final reports of the SangerContig instance.

Usage
## S4 method for signature 'SangerContig'
generateReportSC(
object,
outputDir,
34 SangerContig-class-launchAppSC

includeSangerRead = TRUE,
colors,
navigationAlignmentFN = NULL
)

Arguments
object A SangerContig S4 instance.
outputDir The output directory of the generated HTML report.
includeSangerRead
The parameter that decides whether to include SangerRead level report. The
value is TRUE or FALSE and the default is TRUE.
colors A vector for users to set the colors of (A, T, C, G, else). There are three options
for users to choose from. 1. "default": (green, blue, black, red, purple). 2.
"cb_friendly": ((0, 0, 0), (199, 199, 199), (0, 114, 178), (213, 94, 0), (204, 121,
167)). 3. Users can set their own colors with a vector with five elements.
navigationAlignmentFN
The internal parameter passed to HTML report. Users should not modify this
parameter on their own.

Value
The output absolute path to the SangerContig’s HTML file.

Examples
data("sangerContigData")
## Not run:
generateReportSC(sangerContigData)
generateReportSC(sangerContigData, colors="cb_friendly")
## End(Not run)

SangerContig-class-launchAppSC
launchAppSC

Description
A SangerContig method which launches Shiny app for SangerContig instance.

Usage
## S4 method for signature 'SangerContig'
launchAppSC(object, outputDir = NULL, colors = "default")
SangerContig-class-readTable 35

Arguments

object A SangerContig S4 instance.

outputDir The output directory of the saved new SangerContig S4 instance.
colors A vector for users to set the colors of (A, T, C, G, else). There are three options
for users to choose from. 1. "default": (green, blue, black, red, purple). 2.
"cb_friendly": ((0, 0, 0), (199, 199, 199), (0, 114, 178), (213, 94, 0), (204, 121,
167)). 3. Users can set their own colors with a vector with five elements.

Value

A shiny.appobj object.

Examples

data("sangerContigData")
RShinySC <- launchAppSC(sangerContigData)
RShinySC <- launchAppSC(sangerContigData, colors="cb_friendly")

SangerContig-class-readTable
readTable

Description

A SangerContig method which generates summary table for SangerContig instance

Usage

## S4 method for signature 'SangerContig'

readTable(object, indentation = 0)

Arguments

object A SangerContig S4 instance.

indentation The indentation for different level printing.

Value

None
36 SangerContig-class-updateQualityParam

Examples
data(sangerReadFData)
data(sangerContigData)
data(sangerAlignmentData)
## Not run:
readTable(sangerReadFData)
readTable(sangerContigData)
readTable(sangerAlignmentData)

## End(Not run)

SangerContig-class-updateQualityParam
updateQualityParam

Description
A SangerContig method which updates QualityReport parameter for each the SangerRead instance
inside SangerContig.

Usage
## S4 method for signature 'SangerContig'
updateQualityParam(
object,
TrimmingMethod = "M1",
M1TrimmingCutoff = 1e-04,
M2CutoffQualityScore = NULL,
M2SlidingWindowSize = NULL,
processorsNum = NULL
)

Arguments
object A SangerContig S4 instance.
TrimmingMethod The read trimming method for this SangerRead. The value must be "M1" (the
default) or 'M2'.
M1TrimmingCutoff
The trimming cutoff for the Method 1. If TrimmingMethod is "M1", then the
default value is 0.0001. Otherwise, the value must be NULL.
M2CutoffQualityScore
The trimming cutoff quality score for the Method 2. If TrimmingMethod is 'M2',
then the default value is 20. Otherwise, the value must be NULL. It works with
M2SlidingWindowSize.
SangerContig-class-writeFastaSC 37

M2SlidingWindowSize
The trimming sliding window size for the Method 2. If TrimmingMethod is
'M2', then the default value is 10. Otherwise, the value must be NULL. It works
with M2CutoffQualityScore.
processorsNum The number of processors to use, or NULL (the default) for all available proces-
sors.

Value
A SangerContig instance.

Examples
data("sangerContigData")
## Not run:
updateQualityParam(sangerContigData,
TrimmingMethod = "M2",
M1TrimmingCutoff = NULL,
M2CutoffQualityScore = 40,
M2SlidingWindowSize = 15)
## End(Not run)

SangerContig-class-writeFastaSC
writeFastaSC

Description
A SangerContig method which writes sequences into Fasta files.

Usage
## S4 method for signature 'SangerContig'
writeFastaSC(
object,
outputDir = NULL,
compress = FALSE,
compression_level = NA,
selection = "all"
)

Arguments
object A SangerContig S4 instance.
outputDir The output directory of generated FASTA files.
compress Like for the save function in base R, must be TRUE or FALSE (the default), or a
single string specifying whether writing to the file is to use compression. The
only type of compression supported at the moment is "gzip". This parameter
will be passed to writeXStringSet function in Biostrings package.
38 SangerRead

compression_level
This parameter will be passed to writeXStringSet function in Biostrings pack-
age.
selection This value can be all, reads_alignment, reads_unalignment or contig. It
generates reads and the contig FASTA files.

Value

The output directory of FASTA files.

Examples

data("sangerContigData")
writeFastaSC(sangerContigData)

sangerContigData SangerContig instance

Description

SangerContig instance

Usage

data(sangerContigData)

Author(s)

Kuan-Hao Chao

SangerRead SangerRead

Description

the wrapper function for SangerRead

SangerRead 39

Usage
SangerRead(
printLevel = "SangerRead",
inputSource = "ABIF",
readFeature = "",
readFileName = "",
fastaReadName = NULL,
geneticCode = GENETIC_CODE,
TrimmingMethod = "M1",
M1TrimmingCutoff = 1e-04,
M2CutoffQualityScore = NULL,
M2SlidingWindowSize = NULL,
baseNumPerRow = 100,
heightPerRow = 200,
signalRatioCutoff = 0.33,
showTrimmed = TRUE
)

Arguments
inputSource The input source of the raw file. It must be "ABIF" or "FASTA". The default
value is "ABIF".
readFeature The direction of the Sanger read. The value must be "Forward Read" or "Reverse
Read".
readFileName The filename of the target ABIF file.
fastaReadName If inputSource is "FASTA", then this value has to be the name of the read inside
the FASTA file; if inputSource is "ABIF", then this value is "" by default.
geneticCode Named character vector in the same format as GENETIC_CODE (the default),
which represents the standard genetic code. This is the code with which the
function will attempt to translate your DNA sequences. You can get an appro-
priate vector with the getGeneticCode() function. The default is the standard
code.
TrimmingMethod TrimmingMethod The read trimming method for this SangerRead. The value
must be "M1" (the default) or "M2". M1 is the modified Mott’s trimming algo-
rithm that can also be found in Phred/Phrap and Biopython. M2 is like trimmo-
matic’s sliding window method.
M1TrimmingCutoff
The trimming cutoff for the Method 1. If TrimmingMethod is "M1", then the
default value is 0.0001. Otherwise, the value must be NULL.
M2CutoffQualityScore
The trimming cutoff quality score for the Method 2. If TrimmingMethod is 'M2',
then the default value is 20. Otherwise, the value must be NULL. It works with
M2SlidingWindowSize.
M2SlidingWindowSize
The trimming sliding window size for the Method 2. If TrimmingMethod is
'M2', then the default value is 10. Otherwise, the value must be NULL. It works
with M2CutoffQualityScore.
40 SangerRead-class

baseNumPerRow It defines maximum base pairs in each row. The default value is 100.
heightPerRow It defines the height of each row in chromatogram. The default value is 200.
signalRatioCutoff
The ratio of the height of a secondary peak to a primary peak. Secondary peaks
higher than this ratio are annotated. Those below the ratio are excluded. The
default value is 0.33.
showTrimmed The logical value storing whether to show trimmed base pairs in chromatogram.
The default value is TRUE.

Value
A SangerRead instance.

Author(s)
Kuan-Hao Chao

Examples
inputFilesPath <- system.file("extdata/", package = "sangeranalyseR")
A_chloroticaFdFN <- file.path(inputFilesPath,
"Allolobophora_chlorotica",
"ACHLO",
"Achl_ACHLO006-09_1_F.ab1")
sangerRead <- SangerRead(
printLevel = "SangerRead",
inputSource = "ABIF",
readFeature = "Forward Read",
readFileName = A_chloroticaFdFN,
geneticCode = GENETIC_CODE,
TrimmingMethod = "M1",
M1TrimmingCutoff = 0.0001,
M2CutoffQualityScore = NULL,
M2SlidingWindowSize = NULL,
baseNumPerRow = 100,
heightPerRow = 200,
signalRatioCutoff = 0.33,
showTrimmed = TRUE)

SangerRead-class SangerRead

Description
An S4 class extending sangerseq S4 class which corresponds to a single ABIF file in Sanger se-
quencing.
SangerRead-class 41

Slots
objectResults This is the object that stores all information of the creation result.
inputSource The input source of the raw file. It must be "ABIF" or "FASTA". The default value is
"ABIF".
readFeature The direction of the Sanger read. The value must be "Forward Read" or "Reverse
Read".
readFileName The filename of the target input file.
fastaReadName If inputSource is "FASTA", then this value has to be the name of the read inside
the FASTA file; if inputSource is "ABIF", then this value is NULL by default.
geneticCode Named character vector in the same format as GENETIC_CODE (the default), which
represents the standard genetic code. This is the code with which the function will attempt to
translate your DNA sequences. You can get an appropriate vector with the getGeneticCode()
function. The default is the standard code.
abifRawData An S4 class containing all fields in the ABIF file. It is the abif class defined in
sangerseqR package.
QualityReport A S4 class containing quality trimming related inputs and trimming results.
ChromatogramParam A S4 class containing chromatogram inputs.
primaryAASeqS1 A polypeptide translated from primary DNA sequence starting from the first nu-
cleic acid.
primaryAASeqS2 A polypeptide translated from primary DNA sequence starting from the second
nucleic acid.
primaryAASeqS3 A polypeptide translated from primary DNA sequence starting from the third
nucleic acid.
primarySeqRaw The raw primary sequence from sangerseq class in sangerseqR package before
base calling.
secondarySeqRaw The raw secondary sequence from sangerseq class in sangerseqR package be-
fore base calling.
peakPosMatrixRaw The raw peak position matrix from sangerseq class in sangerseqR package
before base calling.
peakAmpMatrixRaw The raw peak amplitude matrix from sangerseq class in sangerseqR package
before base calling.

Author(s)
Kuan-Hao Chao

Examples
## Simple example
inputFilesPath <- system.file("extdata/", package = "sangeranalyseR")
A_chloroticaFFN <- file.path(inputFilesPath,
"Allolobophora_chlorotica",
"ACHLO",
"Achl_ACHLO006-09_1_F.ab1")
42 SangerRead-class

sangerReadF <- new("SangerRead",

readFeature = "Forward Read",
readFileName = A_chloroticaFFN)

## Input From ABIF file format

# Forward Read
A_chloroticaFFN <- file.path(inputFilesPath,
"Allolobophora_chlorotica",
"ACHLO",
"Achl_ACHLO006-09_1_F.ab1")
sangerReadF <- new("SangerRead",
printLevel = "SangerRead",
inputSource = "ABIF",
readFeature = "Forward Read",
readFileName = A_chloroticaFFN,
fastaReadName = NULL,
geneticCode = GENETIC_CODE,
TrimmingMethod = "M1",
M1TrimmingCutoff = 0.0001,
M2CutoffQualityScore = NULL,
M2SlidingWindowSize = NULL,
baseNumPerRow = 100,
heightPerRow = 200,
signalRatioCutoff = 0.33,
showTrimmed = TRUE)

# Reverse Read
A_chloroticaRFN <- file.path(inputFilesPath,
"Allolobophora_chlorotica",
"ACHLO",
"Achl_ACHLO006-09_2_R.ab1")
sangerReadR <- new("SangerRead",
inputSource = "ABIF",
readFeature = "Reverse Read",
readFileName = A_chloroticaRFN,
geneticCode = GENETIC_CODE,
TrimmingMethod = "M1",
M1TrimmingCutoff = 0.0001,
M2CutoffQualityScore = NULL,
M2SlidingWindowSize = NULL,
baseNumPerRow = 100,
heightPerRow = 200,
signalRatioCutoff = 0.33,
showTrimmed = TRUE)

## Input From FASTA file format

# Forward Read
inputFilesPath <- system.file("extdata/", package = "sangeranalyseR")
A_chloroticaFFNfa <- file.path(inputFilesPath,
"fasta",
"SangerRead",
"Achl_ACHLO006-09_1_F.fa")
SangerRead-class-generateReportSR 43

readNameFfa <- "Achl_ACHLO006-09_1_F"

sangerReadFfa <- new("SangerRead",
inputSource = "FASTA",
readFeature = "Forward Read",
readFileName = A_chloroticaFFNfa,
fastaReadName = readNameFfa,
geneticCode = GENETIC_CODE)
# Reverse Read
A_chloroticaRFNfa <- file.path(inputFilesPath,
"fasta",
"SangerRead",
"Achl_ACHLO006-09_2_R.fa")
readNameRfa <- "Achl_ACHLO006-09_2_R"
sangerReadRfa <- new("SangerRead",
inputSource = "FASTA",
readFeature = "Reverse Read",
readFileName = A_chloroticaRFNfa,
fastaReadName = readNameRfa,
geneticCode = GENETIC_CODE)

SangerRead-class-generateReportSR
generateReportSR

Description
A SangerRead method which generates final reports of the SangerRead instance.

Usage
## S4 method for signature 'SangerRead'
generateReportSR(
object,
outputDir,
colors,
navigationContigFN = NULL,
navigationAlignmentFN = NULL
)

Arguments
object A SangerRead S4 instance.
outputDir The output directory of the generated HTML report.
colors A vector for users to set the colors of (A, T, C, G, else). There are three options
for users to choose from. 1. "default": (green, blue, black, red, purple). 2.
"cb_friendly": ((0, 0, 0), (199, 199, 199), (0, 114, 178), (213, 94, 0), (204, 121,
167)). 3. Users can set their own colors with a vector with five elements.
44 SangerRead-class-MakeBaseCalls

navigationContigFN
The internal parameter passed to HTML report. Users should not modify this
parameter on their own.
navigationAlignmentFN
The internal parameter passed to HTML report. Users should not modify this
parameter on their own.

Value
The output absolute path to the SangerRead’s HTML file.

Examples
data("sangerReadFData")
## Not run:
generateReportSR(sangerReadFData, "~/Documents")
generateReportSR(sangerReadFData, colors="cb_friendly")
## End(Not run)

SangerRead-class-MakeBaseCalls
MakeBaseCalls

Description
A SangerRead method which does base calling on SangerRead instance

Usage
## S4 method for signature 'SangerRead'
MakeBaseCalls(object, signalRatioCutoff = 0.33)

Arguments
object A SangerRead S4 instance.
signalRatioCutoff
The ratio of the height of a secondary peak to a primary peak. Secondary peaks
higher than this ratio are annotated. Those below the ratio are excluded. The
default value is 0.33.

Value
A SangerRead instance.

Examples
data("sangerReadFData")
newSangerReadFData <- MakeBaseCalls(sangerReadFData, signalRatioCutoff = 0.22)
SangerRead-class-qualityBasePlot 45

SangerRead-class-qualityBasePlot
qualityBasePlot

Description
A SangerRead method which creates quality base interactive plot.

Usage
## S4 method for signature 'SangerRead'
qualityBasePlot(object)

Arguments
object A SangerRead S4 instance.

Value
A quality plot.

Examples
data("sangerReadFData")
## Not run:
qualityBasePlot(sangerReadFData)
## End(Not run)

SangerRead-class-readTable
readTable

Description
A SangerRead method which generates summary table for SangerRead instance

Usage
## S4 method for signature 'SangerRead'
readTable(object, indentation = 0)

Arguments
object A SangerRead S4 instance.
indentation The indentation for different level printing.
46 SangerRead-class-updateQualityParam

Value
None

Examples
data(sangerReadFData)
data(sangerContigData)
data(sangerAlignmentData)
## Not run:
readTable(sangerReadFData)
readTable(sangerContigData)
readTable(sangerAlignmentData)

## End(Not run)

SangerRead-class-updateQualityParam
updateQualityParam

Description
A SangerRead method which updates QualityReport parameter inside the SangerRead.

Usage
## S4 method for signature 'SangerRead'
updateQualityParam(
object,
TrimmingMethod = "M1",
M1TrimmingCutoff = 1e-04,
M2CutoffQualityScore = NULL,
M2SlidingWindowSize = NULL
)

Arguments
object A SangerRead S4 instance.
TrimmingMethod The read trimming method for this SangerRead. The value must be "M1" (the
default) or 'M2'.
M1TrimmingCutoff
The trimming cutoff for the Method 1. If TrimmingMethod is "M1", then the
default value is 0.0001. Otherwise, the value must be NULL.
M2CutoffQualityScore
The trimming cutoff quality score for the Method 2. If TrimmingMethod is 'M2',
then the default value is 20. Otherwise, the value must be NULL. It works with
M2SlidingWindowSize.
SangerRead-class-writeFastaSR 47

M2SlidingWindowSize
The trimming sliding window size for the Method 2. If TrimmingMethod is
'M2', then the default value is 10. Otherwise, the value must be NULL. It works
with M2CutoffQualityScore.

Value
A SangerRead instance.

Examples
data("sangerReadFData")
updateQualityParam(sangerReadFData,
TrimmingMethod = "M2",
M1TrimmingCutoff = NULL,
M2CutoffQualityScore = 40,
M2SlidingWindowSize = 15)

SangerRead-class-writeFastaSR
writeFastaSR

Description
A SangerRead method which writes the sequence into Fasta files.

Usage
## S4 method for signature 'SangerRead'
writeFastaSR(
object,
outputDir = NULL,
compress = FALSE,
compression_level = NA
)

Arguments
object A SangerRead S4 instance.
outputDir The output directory of the generated FASTA file.
compress Like for the save function in base R, must be TRUE or FALSE (the default), or a
single string specifying whether writing to the file is to use compression. The
only type of compression supported at the moment is "gzip". This parameter
will be passed to writeXStringSet function in Biostrings package.
compression_level
This parameter will be passed to writeXStringSet function in Biostrings pack-
age.
48 updateQualityParam

Value

The output absolute path to the FASTA file.

Examples
data("sangerReadFData")
writeFastaSR(sangerReadFData)

sangerReadFData SangerRead instance

Description

SangerRead instance

Usage

data(sangerReadFData)

Author(s)

Kuan-Hao Chao

updateQualityParam Method updateQualityParam

Description

Method updateQualityParam

Usage

updateQualityParam(
object,
TrimmingMethod = "M1",
M1TrimmingCutoff = 1e-04,
M2CutoffQualityScore = NULL,
M2SlidingWindowSize = NULL,
...
)
updateQualityParam 49

Arguments
object A QualityReport, SangerRead, SangerContig, or SangerAlignment S4 instance.
TrimmingMethod The read trimming method for this SangerRead. The value must be "M1" (the
default) or 'M2'.
M1TrimmingCutoff
The trimming cutoff for the Method 1. If TrimmingMethod is "M1", then the
default value is 0.0001. Otherwise, the value must be NULL.
M2CutoffQualityScore
The trimming cutoff quality score for the Method 2. If TrimmingMethod is 'M2',
then the default value is 20. Otherwise, the value must be NULL. It works with
M2SlidingWindowSize.
M2SlidingWindowSize
The trimming sliding window size for the Method 2. If TrimmingMethod is
'M2', then the default value is 10. Otherwise, the value must be NULL. It works
with M2CutoffQualityScore.
... Further updateQualityParam-related parameters.

Value
A QualityReport, SangerRead, SangerContig, or SangerAlignment instance.

Examples
data(qualityReportData)
data(sangerReadFData)
data(sangerContigData)
data(sangerAlignmentData)
## Not run:
updateQualityParam(qualityReportData,
TrimmingMethod = "M2",
M1TrimmingCutoff = NULL,
M2CutoffQualityScore = 40,
M2SlidingWindowSize = 15)
updateQualityParam(sangerReadFData,
TrimmingMethod = "M2",
M1TrimmingCutoff = NULL,
M2CutoffQualityScore = 40,
M2SlidingWindowSize = 15)
updateQualityParam(sangerContigData,
TrimmingMethod = "M2",
M1TrimmingCutoff = NULL,
M2CutoffQualityScore = 40,
M2SlidingWindowSize = 15)
updateQualityParam(sangerAlignmentData,
TrimmingMethod = "M2",
M1TrimmingCutoff = NULL,
M2CutoffQualityScore = 40,
M2SlidingWindowSize = 15)
## End(Not run)
50 writeFasta

writeFasta Method writeFasta

Description
A method which writes FASTA files of the SangerRead, SangerContig, and SangerAlignment in-
stance.

Usage
writeFasta(
object,
outputDir = NULL,
compress = FALSE,
compression_level = NA,
selection = "all"
)

Arguments
object A SangerRead, SangerContig, or SangerAlignment S4 instance.
outputDir The output directory of generated FASTA files.
compress Like for the save function in base R, must be TRUE or FALSE (the default), or a
single string specifying whether writing to the file is to use compression. The
only type of compression supported at the moment is "gzip". This parameter
will be passed to writeXStringSet function in Biostrings package.
compression_level
This parameter will be passed to writeXStringSet function in Biostrings pack-
age.
selection This parameter will be passed to writeFastaSC or writeFastaSA.

Value
A SangerRead, SangerContig, or SangerAlignment object.

Author(s)
Kuan-Hao Chao

Examples
data(sangerReadFData)
data(sangerContigData)
data(sangerAlignmentData)
## Not run:
writeFasta(sangerReadFData)
writeFasta(sangerContigData)
writeFastaSA 51

writeFasta(sangerAlignmentData)
## End(Not run)

writeFastaSA Method writeFastaSA

Description
Method writeFastaSA

Usage
writeFastaSA(
object,
outputDir = NULL,
compress = FALSE,
compression_level = NA,
selection = "all"
)

Arguments
object A SangerAlignment S4 instance.
outputDir The output directory of generated FASTA files.
compress Like for the save function in base R, must be TRUE or FALSE (the default), or a
single string specifying whether writing to the file is to use compression. The
only type of compression supported at the moment is "gzip". This parameter
will be passed to writeXStringSet function in Biostrings package.
compression_level
This parameter will be passed to writeXStringSet function in Biostrings pack-
age.
selection This value can be all, contigs_alignment, contigs_unalignment or all_reads.
It generates reads and contigs FASTA files.

Value
The output directory of FASTA files.

Examples
data(sangerAlignmentData)
writeFastaSA(sangerAlignmentData)
52 writeFastaSC

writeFastaSC Method writeFastaSC

Description

Method writeFastaSC

Usage

writeFastaSC(
object,
outputDir = NULL,
compress = FALSE,
compression_level = NA,
selection = "all"
)

Arguments

object A SangerContig S4 instance.

outputDir The output directory of generated FASTA files.
compress Like for the save function in base R, must be TRUE or FALSE (the default), or a
single string specifying whether writing to the file is to use compression. The
only type of compression supported at the moment is "gzip". This parameter
will be passed to writeXStringSet function in Biostrings package.
compression_level
This parameter will be passed to writeXStringSet function in Biostrings pack-
age.
selection This value can be all, reads_alignment, reads_unalignment or contig. It
generates reads and the contig FASTA files.

Value

The output directory of FASTA files.

Examples

data(sangerContigData)
writeFastaSC(sangerContigData)
writeFastaSR 53

writeFastaSR Method writeFastaSR

Description
Method writeFastaSR

Usage
writeFastaSR(
object,
outputDir = NULL,
compress = FALSE,
compression_level = NA
)

Arguments
object A SangerRead S4 instance.
outputDir The output directory of the generated FASTA file.
compress Like for the save function in base R, must be TRUE or FALSE (the default), or a
single string specifying whether writing to the file is to use compression. The
only type of compression supported at the moment is "gzip". This parameter
will be passed to writeXStringSet function in Biostrings package.
compression_level
This parameter will be passed to writeXStringSet function in Biostrings pack-
age.

Value
The output absolute path to the FASTA file.

Examples
data(sangerReadFData)
writeFastaSR(sangerReadFData)
Index

∗ datasets qualityBasePlot,QualityReport-method
qualityReportData, 15 (QualityReport-class-qualityBasePlot),
sangerAlignmentData, 26 13
sangerContigData, 38 qualityBasePlot,SangerRead-method
sangerReadFData, 48 (SangerRead-class-qualityBasePlot),
45
ChromatogramParam-class, 3 QualityReport-class, 12
QualityReport-class-qualityBasePlot,
generateReport, 4 13
generateReportSA, 5 QualityReport-class-updateQualityParam,
generateReportSA,SangerAlignment-method 14
qualityReportData, 15
(SangerAlignment-class-generateReportSA),
22
generateReportSC, 6 readTable, 15
generateReportSC,SangerContig-method readTable,SangerContig-method
(SangerContig-class-generateReportSC), (SangerContig-class-readTable),
33 35
generateReportSR, 7 readTable,SangerRead-method
generateReportSR,SangerRead-method (SangerRead-class-readTable),
(SangerRead-class-generateReportSR), 45
43
SangerAlignment, 16
launchApp, 8 SangerAlignment-class, 19
launchAppSA, 9 SangerAlignment-class-generateReportSA,
launchAppSA,SangerAlignment-method 22
(SangerAlignment-class-launchAppSA), SangerAlignment-class-launchAppSA, 23
23 SangerAlignment-class-updateQualityParam,
launchAppSC, 9 24
launchAppSC,SangerContig-method SangerAlignment-class-writeFastaSA, 25
(SangerContig-class-launchAppSC), sangerAlignmentData, 26
34 sangeranalyseR, 26
SangerContig, 26
MakeBaseCalls, 10 SangerContig-class, 30
MakeBaseCalls,SangerRead-method SangerContig-class-generateReportSC,
(SangerRead-class-MakeBaseCalls), 33
44 SangerContig-class-launchAppSC, 34
SangerContig-class-readTable, 35
ObjectResults-class, 11 SangerContig-class-updateQualityParam,
36
qualityBasePlot, 11 SangerContig-class-writeFastaSC, 37

54
INDEX 55

sangerContigData, 38
SangerRead, 38
SangerRead-class, 40
SangerRead-class-generateReportSR, 43
SangerRead-class-MakeBaseCalls, 44
SangerRead-class-qualityBasePlot, 45
SangerRead-class-readTable, 45
SangerRead-class-updateQualityParam,
46
SangerRead-class-writeFastaSR, 47
sangerReadFData, 48

updateQualityParam, 48
updateQualityParam,QualityReport-method
(QualityReport-class-updateQualityParam),
14
updateQualityParam,SangerAlignment-method
(SangerAlignment-class-updateQualityParam),
24
updateQualityParam,SangerContig-method
(SangerContig-class-updateQualityParam),
36
updateQualityParam,SangerRead-method
(SangerRead-class-updateQualityParam),
46

writeFasta, 50
writeFastaSA, 51
writeFastaSA,SangerAlignment-method
(SangerAlignment-class-writeFastaSA),
25
writeFastaSC, 52
writeFastaSC,SangerContig-method
(SangerContig-class-writeFastaSC),
37
writeFastaSR, 53
writeFastaSR,SangerRead-method
(SangerRead-class-writeFastaSR),
47