R: Create a SNP list object

snpgdsSNPList {SNPRelate}

R Documentation

Create a SNP list object

Description

A list object of SNP information including rs, chr, pos, allele and allele frequency.

Usage

snpgdsSNPList(gdsobj, sample.id=NULL)

Arguments

`gdsobj`	an object of class `SNPGDSFileClass`, a SNP GDS file
`sample.id`	a vector of sample id specifying selected samples; if NULL, all samples are used

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
`afreq`	allele frequency

Author(s)

Xiuwen Zheng

Examples

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

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

# close the file
snpgdsClose(genofile)

[Package SNPRelate version 1.10.2 Index]