snpgdsIBDSelection: Get a table of IBD coefficients

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

Description

Return a data frame with IBD coefficients.

Usage

snpgdsIBDSelection(ibdobj, kinship.cutoff=NaN, samp.sel=NULL)

Arguments

ibdobj	an object of snpgdsIBDClass returned by snpgdsIBDMLE or snpgdsIBDMoM
kinship.cutoff	select the individual pairs with kinship coefficients >= kinship.cutoff; no filter if kinship.cutoff = NaN
samp.sel	a logical vector or integer vector to specify selection of samples

Value

Return a data.frame:

ID1	the id of the first individual
ID2	the id of the second individual
k0	the probability of sharing ZERO alleles
k1	the probability of sharing ONE alleles
kinship	kinship coefficient

Author(s)

Xiuwen Zheng

See Also

snpgdsIBDMLE, snpgdsIBDMoM, snpgdsIBDKING

Examples

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

# YRI population
YRI.id <- read.gdsn(index.gdsn(genofile, "sample.id"))[
	read.gdsn(index.gdsn(genofile, "sample.annot/pop.group"))=="YRI"]
pibd <- snpgdsIBDMoM(genofile, sample.id=YRI.id)
flag <- lower.tri(pibd$k0)
plot(NaN, xlim=c(0,1), ylim=c(0,1), xlab="k0", ylab="k1")
lines(c(0,1), c(1,0), col="red", lty=3)
points(pibd$k0[flag], pibd$k1[flag])

# close the genotype file
closefn.gds(genofile)

# IBD coefficients
dat <- snpgdsIBDSelection(pibd, 1/32)
head(dat)
#       ID1     ID2          k0        k1    kinship
# 1 NA19152 NA19154 0.010749154 0.9892508 0.24731271
# 2 NA19152 NA19093 0.848207777 0.1517922 0.03794806
# 3 NA19139 NA19138 0.010788047 0.9770181 0.25035144
# 4 NA19139 NA19137 0.012900661 0.9870993 0.24677483
# 5 NA18912 NA18914 0.008633077 0.9913669 0.24784173
# 6 NA19160 NA19161 0.008635754 0.9847777 0.24948770

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'.
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 563 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 93 samples, 8,160 SNPs
    using 1 (CPU) core
PLINK IBD:    the sum of all selected genotypes (0,1,2) = 755648
Thu Dec  7 09:07:47 2017    (internal increment: 39424)

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed in 0s
Thu Dec  7 09:07:47 2017    Done.
      ID1     ID2          k0        k1    kinship
1 NA19152 NA19154 0.010749154 0.9892508 0.24731271
2 NA19152 NA19093 0.848207777 0.1517922 0.03794806
3 NA19139 NA19138 0.010788047 0.9770181 0.25035144
4 NA19139 NA19137 0.012900661 0.9870993 0.24677483
5 NA18912 NA18914 0.008633077 0.9913669 0.24784173
6 NA19160 NA19161 0.008635754 0.9847777 0.24948770

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