phenoscanner function

PhenoScanner

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

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).

Returns

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

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

Author(s)

PhenoScanner phenoscanner@gmail.com