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

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:

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(chopsticks)
Loading required package: survival
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/chopsticks/ibs.stats.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ibs.stats
> ### Title: function to calculate the identity-by-state stats of a group of
> ###   samples
> ### Aliases: ibs.stats
> ### Keywords: utilities
> 
> ### ** Examples
> 
> data(testdata)
> result <- ibs.stats(Autosomes[11:20,])
Information: samples = 10, snps = 9445
> summary(result)
     Count         Fraction     
 Min.   :3909   Min.   :0.6164  
 1st Qu.:4014   1st Qu.:0.6265  
 Median :4087   Median :0.6305  
 Mean   :4397   Mean   :0.6303  
 3rd Qu.:4176   3rd Qu.:0.6347  
 Max.   :5762   Max.   :0.6418  
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>