genequeries: phenoscanner genequeries in batches

In jinghuazhao/pQTLtools: A Protein Quantitative Trait Locus Toolkit

phenoscanner genequeries in batches

Description

R/phenoscanner only allows for certain number of items supplied. This simple function return a large number of calls in batches as well as generating SNPIDs.

Usage

genequeries(
  genelist,
  catalogue = "pQTL",
  proxies = "EUR",
  p = 5e-08,
  r2 = 0.8,
  build = 37,
  wait = TRUE
)

Arguments

genelist	a list of SNPs.
catalogue	"None","eQTL","mQTL","methQTL","pQTL","GWAS".
proxies	"None", "AFR","AMR","EAS","EUR","SAS".
p	p value threshold.
r2	r2 for LD.
build	37, 38.
wait	a flag to wait for 1hr for every 50 genes.

Details

Batches are generated and queries are combined into one.

Value

The returned value is a list containing genes and results.

See Also

phenoscanner

Examples

## Not run: 
# single gene
  genequeries("TNFRSF11B")

## End(Not run)

jinghuazhao/pQTLtools documentation built on May 3, 2024, 2:05 p.m.