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

### 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
    snplist <- snpgdsSNPListIntersect(snplist1, snplist2)

    summary(snplist$afreq)

    # close the file
    snpgdsClose(genofile)

[Package SNPRelate version 1.12.2 Index]