R: Identity-By-State (IBS)

snpgdsIBSNum {SNPRelate}

R Documentation

Identity-By-State (IBS)

Description

Calculate the number of SNPs for identity by state for each pair of samples.

Usage

snpgdsIBSNum(gdsobj, sample.id = NULL, snp.id = NULL, autosome.only = TRUE,
    remove.monosnp = TRUE, maf = NaN, missing.rate = NaN, num.thread = 1L,
    verbose = TRUE)

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
`snp.id`	a vector of snp id specifying selected SNPs; if NULL, all SNPs are used
`autosome.only`	if `TRUE`, use autosomal SNPs only; if it is a numeric or character value, keep SNPs according to the specified chromosome
`remove.monosnp`	if TRUE, remove monomorphic SNPs
`maf`	to use the SNPs with ">= maf" only; if NaN, no MAF threshold
`missing.rate`	to use the SNPs with "<= missing.rate" only; if NaN, no missing threshold
`num.thread`	the number of (CPU) cores used; if `NA`, detect the number of cores automatically
`verbose`	if TRUE, show information

Details

The minor allele frequency and missing rate for each SNP passed in snp.id are calculated over all the samples in sample.id.

Value

Return a list (n is the number of samples):

`sample.id`	the sample ids used in the analysis
`snp.id`	the SNP ids used in the analysis
`ibs0`	a n-by-n matrix, the number of SNPs sharing 0 IBS
`ibs1`	a n-by-n matrix, the number of SNPs sharing 1 IBS
`ibs2`	a n-by-n matrix, the number of SNPs sharing 2 IBS

Author(s)

Xiuwen Zheng

Examples

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

RV <- snpgdsIBSNum(genofile)
pop <- read.gdsn(index.gdsn(genofile, "sample.annot/pop.group"))
L <- order(pop)
image(RV$ibs0[L, L]/length(RV$snp.id))

# close the genotype file
snpgdsClose(genofile)

[Package SNPRelate version 1.10.2 Index]