catalogueR-package: Rapid querying, colocalization, and plotting of summary stats...

In RajLabMSSM/catalogueR: QTL data extraction and colocalization

Rapid querying, colocalization, and plotting of summary stats from the eQTL Catalogue.

Description

The functions in catalogueR are partly derived from the following eQTL Catalogue tutorial. Additional eQTL Catalogue Resources:

• GitHub

• In-depth API documentation

• FTP server

Details

Notes on parallelization: There's multiple levels to parallelize on. You can only choose one level at a time:

multithread_qtl=TRUE

Across QTL datasets

multithread_loci=TRUE

Across loci

multithread_tabix=TRUE

Within tabix files

You can also get a speedup by using tabix instead of the rest API Test: For 3 loci, and X QTL datasets:

RESTful API:

7.5 minutes

Tabix:

27 seconds (*clear winner! ~17x speedup)

That said, if you're only query a small number of specific SNPs (rather than a large range), the RESTful API can sometimes be faster.

Author(s)

Maintainer: Brian Schilder [e-mail] (ORCID)

Authors:

• Jack Humphrey [e-mail] (ORCID)

• Towfique Raj [e-mail] (ORCID)

See Also

Useful links:

• https://github.com/RajLabMSSM/catalogueR

• Report bugs at https://github.com/RajLabMSSM/catalogueR/issues

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