[R-sig-genetics] Re : Calcualtion of pairwise relatedness in R: > package?

Neil Shephard nshephard at gmail.com
Mon Jun 28 15:00:16 CEST 2010

On Mon, Jun 28, 2010 at 12:04 PM, Nevil Amos <nevil.amos at gmail.com> wrote:
> Thanks for the offer Ross,
> I'm looking at 8-18 locus microsat data.  I can undertake the calculations
> easily enough elsewhere,.  However if there was a function out there already
> I would have used it since most of my data manipulation and calculations are
> being handled in R: and it would have made things neater.

You could format and prepare your data within R, output to a text file
and then make a system call to your external program(s) from within R
to perform the calculations before reading them back into R for
summarising and presenting.

A bit of work I'd imagine, but I'd guess it has the potential of being
developed into a package for subsequent use by yourself and others.

Also whilst typing that I remembered that Shaun Purcell's Plink (see
http://pngu.mgh.harvard.edu/~purcell/plink/) has some integration with
R, although its mainly geared towards analysis of SNPs and CNVs (but
given that it can handle multi-marker haplotypes it should be capable
of handling multi-allelic microsatellites).


"... no scientific worker has a fixed level of significance at which
from year to year, and in all circumstances, he rejects hypotheses; he
rather gives his mind to each particular case in the light of his
evidence and his ideas." - Sir Ronald A. Fisher (1956)

Email - nshephard at gmail.com
Website - http://slack.ser.man.ac.uk/
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