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

snpgdsSNPListIntersect {SNPRelate}

R Documentation

Get a common SNP list between two SNP list objects

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

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
snplist <- snpgdsSNPListIntersect(snplist1, snplist2)

summary(snplist$afreq)

# close the file
snpgdsClose(genofile)

[Package SNPRelate version 1.10.2 Index]