[R] Re: QTL interval mapping in outbred populations

[David Duffy]

On Mon, 8 Nov 2004 ssim at lic.co.nz wrote:
>
> Is there an add-on package in R for QTL interval mapping for outbred
> population, eg. Haley-Knott regression method ?
>
> Stella

I believe Karl Broman's R/QTL (http://biosun01.biostat.jhsph.edu/~kbroman/software/)
and Brian Yandell's bim (http://www.stat.wisc.edu/~yandell/qtl/software/),
Richard Mott's happyR (http://www.well.ox.ac.uk/happy/happyR.shtml)
are mainly for experimental crosses, but do multipoint analyses.

You might also try QTL Express (http://qtl.cap.ed.ac.uk/), or if you are
analysing smaller families, programs like MERLIN (Goncalo Abecasis's).

For outbred families from natural populations, the estimation of
multipoint ibd sharing can be done by various programs like MERLIN,
LOKI, SIMWALK2 etc and the resulting kinship matrices can be imported
into R.  It's pretty easy to write a variance components or regression
based QTL routine to analyse them.  The programs by Jing hua Zhao, Beth
Atkinson and others could also then be used for linkage analysis of
survival data (http://www.ucl.ac.uk/~rmjdjhz/r-progs.htm) (I haven't any
experience with these programs yet).

David Duffy.

| David Duffy (MBBS PhD)                                         ,-_|\
| email: davidD at qimr.edu.au  ph: INT+61+7+3362-0217 fax: -0101  /     *
| Epidemiology Unit, Queensland Institute of Medical Research   \_,-._/
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