ibs.stats {chopsticks} | R Documentation

## function to calculate the identity-by-state stats of a group of samples

### Description

Given a snp.matrix-class or a X.snp.matrix-class object with $N$ samples, calculates some statistics about the relatedness of every pair of samples within.

### Usage

    ibs.stats(x)

### Arguments

`x` | a snp.matrix-class or a X.snp.matrix-class object containing $N$ samples

### Details

No-calls are excluded from consideration here.

### Value

A data.frame containing $N (N-1)/2$ rows, where the row names are the sample name pairs separated by a comma, and the columns are:

`Count` | count of identical calls, exclusing no-calls
`Fraction` | fraction of identical calls comparied to actual calls being made in both samples

### Warning

In some applications, it may be preferable to subset a (random) selection of SNPs first - the calculation time increases as $N (N-1) M /2$ . Typically for N = 800 samples and M = 3000 SNPs, the calculation time is about 1 minute. A full GWA scan could take hours, and quite unnecessary for simple applications such as checking for duplicate or related samples.

### Note

This is mostly written to find mislabelled and/or duplicate samples.

Illumina indexes their SNPs in alphabetical order so the mitochondria SNPs comes first - for most purpose it is undesirable to use these SNPs for IBS purposes.

TODO: Worst-case S4 subsetting seems to make 2 copies of a large object, so one might want to subset before rbind(), etc; a future version of this routine may contain a built-in subsetting facility to work around that limitation.

### Author(s)

Hin-Tak Leung htl10@users.sourceforge.net

### Examples

    data(testdata)
    result <- ibs.stats(Autosomes[11:20,])
    summary(result)

[Package chopsticks version 1.46.0 Index]