SNPRelate (version 1.6.4)

snpgdsIBSNum: 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 = 1, 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 "

num.thread

the number of (CPU) cores used; if NA, detect the number of cores automatically

verbose

if TRUE, show information

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

Details

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

See Also

snpgdsIBS

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)