get.snps.geuvadis: Get SNP data (Geuvadis)

In rauschenberger/spliceQTL: Alternative Splicing

Description

This function transforms SNP data (local machine): downloads missing genotype data from ArrayExpress, transforms variant call format to binary files, removes SNPs with low minor allele frequency, labels SNPs in the format "chromosome:position", changes sample identifiers

Usage

get.snps.geuvadis(chr, data = NULL, path = getwd())

Arguments

chr	chromosome: integer 1-22
data	local directory for VCF (variant call format) and SDRF (sample and data relationship format) files;
path	local directory for output

Examples

path <- "C:/Users/a.rauschenbe/Desktop/spliceQTL/data"

rauschenberger/spliceQTL documentation built on May 13, 2019, 3:02 a.m.