geneGrep: Gene ID query

In tgirke/longevityTools: Analysis tools for longevity research

Description

The geneGrep function subsets an eQTL data set (data.frame) from GTEx with a vector of gene IDs as arguments. Genes without significant eSNPs are removed from results.

Usage

geneGrep(dat, genes)

Arguments

dat	Object of class data.frame.
genes	Gene IDs stored in character vector.

Value

Object of class data.frame.

Author(s)

Dan Evans

See Also

read.delim

Examples

library(longevityTools)
## Download of eQTL data from GTEx: http://www.gtexportal.org/home/datasets
## Note, this downloads a 1.3GB file, which will take some time.

## Not run: 
download.file("http://www.gtexportal.org/static/datasets/gtex_analysis_v6/single_tissue_eqtl_data/GTEx_Analysis_V6_eQTLs.tar.gz", "./GTEx_Analysis_V6_eQTLs.tar.gz")
untar("GTEx_Analysis_V6_eQTLs.tar.gz")

## End(Not run)
## The following sample file 'Whole_Blood_Analysis.snpgenes' was subsetted to the first 100 rows
samplepath <- system.file("extdata", "Whole_Blood_Analysis.snpgenes.head100", package="longevityTools") 
dat <- read.delim(samplepath)
myGenes <- c("RP11-693J15.4", "RP11-809N8.4", "junkNoMatch")
result <- geneGrep(dat, myGenes)

tgirke/longevityTools documentation built on May 31, 2019, 9:07 a.m.