SNP2gene: Maps SNPs to their nearest genes

In BaderLab/POPPATHR: Population-based pathway analysis of SNP-SNP coevolution

Description

NOTE: updated GenomicRanges to version 1.30.1 on 01/30/2018 Requires ignore.strand=TRUE param to properly run distanceToNearest() given unknown strand assignment for SNP array-based genotyping info

Usage

SNP2gene(in_file, refgene_file, marg = 0, output_file)

Arguments

in_file	(char) path to PLINK bim file (only CHR, SNP, and BP columns considered).
refgene_file	(char) path to refseq table with header.
marg	(integer) region upstream and downstream of [txStart,txEnd] (default=0).
output_file	(char) path to write snp-to-gene mapping file.

Value

none

BaderLab/POPPATHR documentation built on Dec. 17, 2021, 9:53 a.m.