PhenoScanner

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

PhenoScanner <phenoscanner@gmail.com>

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