Re: ASReml discussion group

Dear Mike,

Greetings,

Well yes, there is a steep learning curve, because ASReml can handle quite
a range of special situations, as well as the traditional ones.
On the VSN website is a set of 16 .mp3 files with accompanying slides,
based on ASReml courses I have run.
They run about 15 minutes each and cover all the basic stuff.

Also, could you help out a bit on the learning curve part with a couple of
specimen scripts?

Check out the 'Cookbook' site listed below.

How about 1) a straightforward bivariate animal model analysis with
sire/maternal grandsire pedigree to estimate heritabilities, genetic and
environmental correlations;

 and 2) a similar analysis with one trait recorded on bulls and the second
recorded on heifers so that the environmental correlation is zero? For the
purpose of illustration the models could include only a single fixed
effect, say contemporary groups, which would have many levels and thus be
invoked with the !f option in the model specification.

Well both examples are in the following job, assuming the same data file

The following job will run both

!RENAME !ARG 1 2 # Rename cause the job to run twice and
renames output files ...1 and ...2
!DOPART $1 # First run, $1 is 1 and first PART is
processed; Second run $1 is 2 and the second part is processed
Maternal Grandsire model
  ID !P # ID will be coded as defined by the pedigree
file
  Sex !A # Sex coded in second field of Data as 'M' and
'F' say
  Cgroup !I 1000 # I expect about 1000 contemporary groups; they have
an integer number as a group identifier
  bwt !M0 # birthweights of zero are to be treated as missing
values
  ywt !M0
  Mtrait !M 0 # A trait only measured on males
  Ftrait !M 0 # A trait only measured on females

MGS.ped !skip 1 !MGS !ALPHA #The pedigree file has a header line like
Animal Sire MGrandSire and identities are alhanumeric (up to 20
characters)
datafile.dat !skip 1 # data file has a heading line to skip (like
Animal Sex CGroup bwt wwt Mtrait Ftrait)

!PART 1
 bwt ywt ~ Trait Trait.Sex !r Trait.ID !f Trait.Cgroup
1 2 1
0
Trait 0 US !GP # Residual variance structure
3*0 # lets ASReml work out initial values else say 25 20 95
Trait.ID 2
Trait 0 US !GP # Genetic variance structure
3*0 # lets ASReml work out initial values else say 2.5 2.0 9.5
ID 0 AINV

!PART 2
 Mtrait Ftrait ~ Trait Trait.Sex !r Trait.ID !f Trait.Cgroup
1 2 1
0
Trait 0 US !GPZP # Residual variance structure
3*0 # lets ASReml work out initial values else say 25 0 95
Trait.ID 2
Trait 0 US !GP # Genetic variance structure
3*0 # lets ASReml work out initial values else say 2.5 2.0 9.5
ID 0 AINV

After this has run and converged, you might like to use a .pin file

F PhenVar 1:3 + 4:6
H h2_bwt 4 7
H h2_ywt 6 9
R rg 4:6

So if the former file is mgsrun.as and the latter is mgsrun.pin

ASReml -W1 mgsrun

from the command propmt will fit the models,

ASReml -Pmgsrun1 mgsrun
ASReml -Pmgsrun2 mgsrun

will then calculate the heritabilities.

May Jesus Christ be gracious to you,

Arthur Gilmour, His servant .

Mixed model regression mapping for QTL detection in experimental crosses.
Computational Statistics and Data Analysis 51:3749-3764 now available at
http://dx.doi.org/10.1016/j.csda.2006.12.031

Profile: http://www.dpi.nsw.gov.au/reader/17263
Personal website: http://www.cargovale.com.au/

mailto:Arthur.Gilmour_at_dpi.nsw.gov.au, arthur_at_cargovale.com.au
Principal Research Scientist (Biometrics)
NSW Department of Primary Industries
Orange Agricultural Institute, Forest Rd, ORANGE, 2800, AUSTRALIA

fax: 02 6391 3899; 02 6391 3922 Australia +61
telephone work: 02 6391 3815; home: 02 6364 3288; mobile: 0438 251 426

ASREML 2 is now available from http://www.VSNi.co.uk/products/asreml
The ASReml discussion group is at ASREML-L_at_dpi.nsw.gov.au
To join it, mailto:arthur.gilmour_at_dpi.nsw.gov.au
Archives are at
https://gatekeeper.dpi.nsw.gov.au/Listserv/archives/asreml-l.html
Cookbook: http://uncronopio.org/ASReml

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Leave 10 Aug - 15 Aug
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Received on Mon Sep 20 2007 - 12:48:09 EST