snpgdsIBDSelection {SNPRelate} | R Documentation

## Get a table of IBD coefficients

### 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 <- 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

[Package SNPRelate version 1.26.0 Index]