eQTLcatalogue_example_queries: Paths to example eQTL Catalogue query results

In RajLabMSSM/catalogueR: QTL data extraction and colocalization

Paths to example eQTL Catalogue query results

Description

Returns the paths to eQTL Catalogue query results stored within catalogueR. Each file is a merged data.table of the GWAS summary stats used to make the query, and the eQTL Catalogue query results (which can contain data for multiple eGenes).

Usage

eQTLcatalogue_example_queries(
  save_dir = tempdir(),
  fnames = c("BST1__Alasoo_2018.macrophage_IFNg+Salmonella.tsv.gz",
    "BST1__Alasoo_2018.macrophage_IFNg.tsv.gz",
    "BST1__Alasoo_2018.macrophage_naive.tsv.gz",
    "BST1__Alasoo_2018.macrophage_Salmonella.tsv.gz",
    "LRRK2__Alasoo_2018.macrophage_IFNg.tsv.gz",
    "LRRK2__Alasoo_2018.macrophage_naive.tsv.gz",
    "MEX3C__Alasoo_2018.macrophage_IFNg.tsv.gz",
    "MEX3C__Alasoo_2018.macrophage_naive.tsv.gz")
)

Arguments

save_dir	Local directory to cache data in.
fnames	Character vector of file names to download.

Details

GWAS data originally comes from the Parkinson's disease GWAS by Nalls et al., 2019 (The Lancet Neurology).

Value

Path to merged example GWAS-QTL summary statistics.

Source

https://doi.org/10.1016/S1474-4422(19)30320-5

paths <- catalogueR:::eQTLcatalogue_example_queries_local() fnames <- lapply(paths, function(x){ piggyback::pb_upload(file = x, repo = "RajLabMSSM/catalogueR") return(basename(x)) })

Examples

gwas.qtl_paths <- catalogueR::eQTLcatalogue_example_queries()

RajLabMSSM/catalogueR documentation built on Jan. 1, 2023, 10:45 a.m.