pronoy2108 / phenoscanner

phenoscanner allows users to query the PhenoScanner database of genotype-phenotype associations from inside R

phenoscanner

phenoscanner allows users to query the PhenoScanner database of genotype-phenotype associations from inside R.

Functions

• phenoscanner - this function allows users to query the PhenoScanner database from inside R

Installation

1. install.packages("devtools")
2. library(devtools)
3. install_github("phenoscanner/phenoscanner")
4. library(phenoscanner)

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

Citations

• Staley JR, et al. PhenoScanner: a database of human genotype-phenotype associations. Bioinformatics 2016;32(20):3207-3209.
• Kamat MA, et al. PhenoScanner V2: an expanded tool for searching human genotype-phenotype associations. Bioinformatics 2019;35(22):4851-4853.

Terms of use

Please abide by the terms of use of PhenoScanner when using this R package.