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

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)

[Package SNPRelate version 1.10.2 Index]