phenoscanner: phenoscanner

In phenoscanner/phenoscanner: R package to query PhenoScanner from R

Description

phenoscanner 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$results)
res$genes

# Region
res <- phenoscanner(regionquery="chr11:9685624-9774538")
head(res$results)
res$regions
  
# To query multiple SNPs, genes or regions, please supply a vector of SNPs, genes or regions
# to snpquery, genequery or regionquery options, respectively. For example, to query multiple SNPs:   
res <- phenoscanner(snpquery=c("rs10840293","rs10"))  
head(res$results)  
res$snps 

phenoscanner/phenoscanner documentation built on Aug. 10, 2020, 2:40 p.m.