Re: Random SNP effects

Thanks Arthur, processing through ASReml3 looks particularly helpful.
Many regards

--
Denis Fidalis Mujibi
Ph. D. Candidate
Department of Agriculture, Food and Nutritional Science
4-10 AgroForestry Centre
University of Alberta, Edmonton
T6G2P5, AB, Canada.
Quoting arthur.gilmour_at_DPI.NSW.GOV.AU:
> Dear Denis,
>
> Concerning:
> I was intending to run a random SNP model to estimate the variance of
> total phenotypic variance accounted for by the SNP. For simplicity, I
> would like to assume an IID structure for the SNP.
> I was wondering if the following model definition captures this.
>
> Trait ~ mu fixed_effects !r id snp1 !f contemp
> 0 0 1
> id 2
> 1 0 US 0.4 !GP
> id
>
> Also would there be a way to make ASReml output the Sum of Squares in
> the .asr file?
>
>
> You can write the model in that way, but the last 4 lines are unnecessary
> as the model specified is the default model.
> i.e.
>
> Trait ~ mu fixed_effects !r id 0.4 !GP snp1 !f contemp
>
>
> specifies the same model.
>
>
> Now if you have a relatively large number of SNPs you want to fit in this
> way, there are some tricks available in ASReml3
> to make this easier (i.e. faster).  In particular, there is a large
> overhead reading the data if you have to read 1000 SNP
> variables from the data file, and then only use a few in the model, and
> you do this 1000 times.  So if you put the SNP data
> in separate files and use !MBF to just access the particular SNPs you
> want, this speeds the processing.
>
> Further, the !CYCLE command has been extended so it is easier to cycle
> through the say 1000 models taking one SNP each cycle.
> And a summary line is written to the .asr file which can be extracted by
> the unix utility 'grep' and sorted to identify the best fits.
>
> Now, concerning the Sum of Squares: it cannot be directly extracted but
> you can calculate an equivalent statistic from the
> Residual variance which is reported along with the REML LogL.
>
> The asreml3alpha download registration page is:
> http://www.austatgen.org/asreml3alpha.php
> There are asreml3alpha forums at:   http://www.austatgen.org/asreml3forum
>
> May  Jesus Christ be gracious to you in 2008,
>
> Arthur Gilmour, His servant .
>
> Mixed model regression mapping for QTL detection in experimental crosses.
> Computational Statistics and Data Analysis 51:3749-3764 at
> http://dx.doi.org/10.1016/j.csda.2006.12.031
>
> Profile:http://www.dpi.nsw.gov.au/research/staff/arthur-gilmour
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>
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> Principal Research Scientist (Biometrics)
> NSW Department of Primary Industries
> Orange Agricultural Institute,  Forest Rd, ORANGE, 2800, AUSTRALIA
>
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