snpgdsSNPList: Create a SNP list object

In SNPRelate: Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data

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:

snp.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

See Also

snpgdsSNPListIntersect

Examples

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

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

# close the file
snpgdsClose(genofile)

SNPRelate documentation built on Nov. 8, 2020, 5:31 p.m.