snpgdsIBSNum: The numbers of Identity-By-State (IBS) SNPs

In SNPRelate: Parallel Computing Toolset for Genome-Wide Association Studies (GWAS)

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	a GDS file object (gds.class)
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
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
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 <- openfn.gds(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
closefn.gds(genofile)

Example output

Loading required package: gdsfmt
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
Hint: it is suggested to call `snpgdsOpen' to open a SNP GDS file instead of `openfn.gds'.
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
Mon Apr 23 13:24:44 2018    (internal increment: 13056)

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Mon Apr 23 13:24:44 2018    Done.

SNPRelate documentation built on May 2, 2019, 4:56 p.m.