README.md

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

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