Description Usage Arguments Value Author(s) See Also Examples
Return a data frame with IBD coefficients.
1 | snpgdsIBDSelection(ibdobj, kinship.cutoff=NaN, samp.sel=NULL)
|
ibdobj |
an object of |
kinship.cutoff |
select the individual pairs with kinship coefficients
>= kinship.cutoff; no filter if |
samp.sel |
a logical vector or integer vector to specify selection of samples |
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 |
Xiuwen Zheng
snpgdsIBDMLE
, snpgdsIBDMoM
,
snpgdsIBDKING
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 | # open an example dataset (HapMap)
genofile <- snpgdsOpen(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
snpgdsClose(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
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