R: Switch allele strand.

snpgdsSNPListStrand {SNPRelate}

R Documentation

Switch allele strand.

Description

To get a logical vector, indicating whether allele references of snplist2 need to be switched, with respect to snplist1.

Usage

snpgdsSNPListStrand(snplist1, snplist2, same.strand=FALSE)

Arguments

`snplist1`	the first SNP list object “snpgdsSNPListClass”
`snplist2`	the second SNP list object “snpgdsSNPListClass”
`same.strand`	`TRUE` assuming alleles are on the same strand (e.g., forward strand); otherwise, `FALSE` not assuming whether on the same strand or not

Value

a logical vector, where TRUE indiciates the allele references need to be switched, and NA indiciates that locus is not in the common snp list.

Author(s)

Xiuwen Zheng

Examples

# open an example dataset (HapMap)
genofile <- snpgdsOpen(snpgdsExampleFileName())

# to get a snp list object
snplist1 <- snpgdsSNPList(genofile)
snplist2 <- snpgdsSNPList(genofile)

# a common snp list
L <- snpgdsSNPListStrand(snplist1, snplist2)

table(L, exclude=NULL)

# close the file
snpgdsClose(genofile)

[Package SNPRelate version 1.10.2 Index]