select_gtex_tissues: Get the GTEx files corresponding to the tissues of interest

In MCorentin/vargen: Fetching Variants Related to Phenotypes Using Public Databases

Get the GTEx files corresponding to the tissues of interest

Description

Use list_gtex_tissues to get the list of GTEx files and their associated keywords. Grep the user's query against the list of keywords (case is ignored) to return all the corresponding tissue files. eg: "adipose" will return the files corresponding to "Adipose_Subcutaneous" AND "Adipose_Visceral_Omentum". The tissues in the query are grepped one after the other. If one of the keywords does not correspond to any tissues, stop is called and an error message is displayed.

Usage

select_gtex_tissues(gtex_dir, tissues_query = "")

Arguments

gtex_dir	is the directory contaning the files from "GTEx_Analysis_v8_eQTL.tar.gz" (cf: https://gtexportal.org/home/datasets)
tissues_query	is a vector of keywords to select the tissues of interest (eg: "adipose", "brain", "Heart_Left_Ventricle"). NOT case sensitive. (default: "", return everything)

Value

the list of files corresponding to the tissues of interest

Examples

vargen_install(install_dir = "./vargen_data/")
select_gtex_tissues("./vargen_data/GTEx_Analysis_v8_eQTL/",
                    c("adipose", "Heart_Left_Ventricle", "leg"))

select_gtex_tissues("./vargen_data/GTEx_Analysis_v8_eQTL/",
                    "brain")

MCorentin/vargen documentation built on Feb. 6, 2024, 2:32 p.m.