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

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/IBS.r

Description

Calculate the number of SNPs for identity by state for each pair of samples

Usage

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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

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# 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 31, 2017, 2:40 a.m.