SNPRelate (version 1.6.4)

snpgdsSNPListStrand: 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.

See Also

snpgdsSNPList, snpgdsSNPListStrand

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)