patch_strand: function to change strand

In GenABEL: genome-wide SNP association analysis

Description

Changes strand in gwaa.data-class object

Usage

	patch_strand(data,snpid,strand,based_on="snpnames", quiet = TRUE)

Arguments

data	gwaa.data or snp.data object
snpid	vector of ids of snsp (name or position)
strand	vector of strands ("+","-","u")
based_on	either "snpnames" or "map" depending on what info is provided by snpid
quiet	indicates if recoding report should be directed to the screen

Details

For SNPs, as identified by 'snpid', changes strand to strand specified by 'strand'

Value

object of gwaa.data or snp.data class

Author(s)

Yurii Aulchenko

Examples

require(GenABEL.data)
data(srdta)
as.character(srdta@gtdata@strand[1:20])
a <- patch_strand(srdta,srdta@gtdata@snpnames[1:10],rep("+",10))
as.character(a@gtdata@strand[1:20])
a <- patch_strand(srdta,srdta@gtdata@map[1:10],rep("+",10),based_on="map")
as.character(a@gtdata@strand[1:20])

GenABEL documentation built on May 30, 2017, 3:36 a.m.