miRQTL: microRNA eQTL analysis pipeline
The code base is plug and play, there is no need to install the pipeline (unless otherwise specified). This project is a beta version and will be tweaked in the future for more controls.
Download the repository by navigating to code and select download zip.
Once downloaded, change directory to TWAS and type python twas_pipeline.py -h
python twas_pipeline.py -h
usage: twas_pipeline.py [-h] {GCTA,fusionWTS,fusionAssoc} ...
TWAS - pipeline for GCTA and fusion analysis.
positional arguments:
{GCTA,fusionWTS,fusionAssoc}
Choose a module to run
GCTA Run Genome-wide Complex Trait Analysis (GCTA) analysis
fusionWTS Create Fusion - weights
fusionAssoc Create Fusion - association
optional arguments:
-h, --help show this help message and exit
Selcet the module you prefer and see more options. For example if you prefer to peform GCTA analysis:
python twas_pipeline.py GCTA -h
usage: twas_pipeline.py GCTA [-h] --exprn EXPRN --genotype GENOTYPE --covar COVAR --output OUTPUT [--threads THREADS]
optional arguments:
-h, --help show this help message and exit
--exprn EXPRN Input expression file. Example: ./test_input/dlpfc-cauc_miRNA_expr.bed
--genotype GENOTYPE The genotype data in PLINK format. Example: ./test_input/dlpfc-cauc_genotype
--covar COVAR Input covariates file. Example: ./test_input/dlpfc-cauc_plinkCovariates.txt
--output OUTPUT The working directory for saving intermediate and results. Example: GCTA
--threads THREADS Number of threads
NOTE: Some files like GWAS traits and input test Genotype can't be loaded due to limit in file size and/or data privacy.
For more information, please contact:
Dr. Taeyoung Hwang,
Lieber Institute for Brain Development,
Johns Hopkins University, Baltimore, MD. USA - 21205.