snpgdsIBSNum: Identity-By-State (IBS)

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

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)

Example output

Loading required package: gdsfmt
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
Identity-By-State (IBS) analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
    using 1 (CPU) core
IBS:    the sum of all selected genotypes (0,1,2) = 2446510
Fri Apr 27 13:08:37 2018    (internal increment: 13056)

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed in 0s
Fri Apr 27 13:08:37 2018    Done.

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