snpgdsSNPListIntersect: Get a common SNP list between two SNP list objects

In SNPRelate: Parallel Computing Toolset for Genome-Wide Association Studies (GWAS)

Description

Get a common SNP list by comparing their rs id, chromosome indices and positions.

Usage

snpgdsSNPListIntersect(snplist1, snplist2)

Arguments

snplist1	the first SNP list object snpgdsSNPListClass
snplist2	the second SNP list object snpgdsSNPListClass

Value

Return an object of “snpgdsSNPListClass” including the following components:

rs.id	SNP id
chromosome	SNP chromosome index
position	SNP physical position in basepair
allele	reference / non-ref alleles from the first SNP list object
afreq	allele frequency from the first SNP list object

Author(s)

Xiuwen Zheng

See Also

snpgdsSNPList, snpgdsSNPListStrand

Examples

# open an example dataset (HapMap)
genofile <- openfn.gds(snpgdsExampleFileName())

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

# a common snp list
snplist <- snpgdsSNPListIntersect(snplist1, snplist2)

summary(snplist$afreq)

# close the genotype file
closefn.gds(genofile)

SNPRelate documentation built on May 2, 2019, 4:56 p.m.