snpgdsIBS: Identity-By-State (IBS) proportion

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

Description

Calculate the fraction of identity by state for each pair of samples

Usage

snpgdsIBS(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.

The values of the IBS matrix range from ZERO to ONE.

Value

Return a list (class "snpgdsIBSClass"):

sample.id	the sample ids used in the analysis
snp.id	the SNP ids used in the analysis
ibs	a matrix of IBS proportion, "# of samples" x "# of samples"

Author(s)

Xiuwen Zheng

See Also

snpgdsIBSNum

Examples

# open an example dataset (HapMap)
genofile <- openfn.gds(snpgdsExampleFileName())

# perform identity-by-state calculations
ibs <- snpgdsIBS(genofile)

# perform multidimensional scaling analysis on the genome-wide IBS pairwise distances:
loc <- cmdscale(1 - ibs$ibs, k = 2)
x <- loc[, 1]; y <- loc[, 2]
race <- as.factor(read.gdsn(index.gdsn(genofile, "sample.annot/pop.group")))
plot(x, y, col=race, xlab = "", ylab = "", main = "cmdscale(IBS Distance)")
legend("topleft", legend=levels(race), text.col=1:nlevels(race))

# 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 Aug 27 15:58:26 2018    (internal increment: 13056)

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Mon Aug 27 15:58:26 2018    Done.

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