phenoscanner: PhenoScanner

In MendelianRandomization: Mendelian Randomization Package

PhenoScanner

Description

The phenoscanner function queries the PhenoScanner database of genotype-phenotype associations from inside R.

Usage

phenoscanner(
  snpquery = NULL,
  genequery = NULL,
  regionquery = NULL,
  catalogue = "GWAS",
  pvalue = 1e-05,
  proxies = "None",
  r2 = 0.8,
  build = 37
)

Arguments

snpquery	a vector of SNPs.
genequery	a vector of gene names.
regionquery	a vector of genomic regions.
catalogue	the catalogue to be searched (options: None, GWAS, eQTL, pQTl, mQTL, methQTL).
pvalue	the p-value threshold.
proxies	the proxies database to be searched (options: None, AFR, AMR, EAS, EUR, SAS).
r2	the r2 threshold.
build	the genome build (options: 37, 38).

Value

a list containing a data.frame of association results and a data.frame of SNP/Region/Gene information from PhenoScanner.

Author(s)

PhenoScanner <[e-mail]>

Examples

# SNP
# res <- phenoscanner(snpquery="rs10840293")
# head(res$results)
# res$snps

# Gene
# res <- phenoscanner(genequery="SWAP70")
# head(res$results)
# res$snps

# Region
# res <- phenoscanner(regionquery="chr11:9685624-9774538")
# head(res$results)
# res$regions

MendelianRandomization documentation built on Aug. 9, 2023, 1:05 a.m.