R help - Dec 2004 - Re : LOOPS

Dear lists,

I want to construct a loop in R, but don't know how to do it. I can do it
in SAS, but I prefer in R  (which I am hoping I will off SAS for good
soon). Could anyone help me to convert the SAS codes to equivalent R codes.

Basically, the following codes were written to establish the sire gametes
or phases for daughter design for one markers two alleles.

Here are the SAS code:

do i=1 to 744;
      do j=745 to 1540;
            m[j]=0;
            if sire[j]=anml[i] then do;
                if m1[j]=m1[i]  and m2[j]=m2[i] then m[j]=0;
                else if m1[j]=m1[i] then m[j] =1;
                else if m1[j]=m2[i] then m[j==2;
                else if m2[j]=m1[i] then m[j]=1;
                else if m2[j]=m2[i] then m[j]=2;
                else m[j]=0;
            end do;
     end;
end;


Thanks Stella
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Thanks Peter.

Basically, I am trying to establish the line of  marker allele the progeny
has inherited from either the sire or the dam.  The progeny will share the
sires but each have different dam (ie., daughter design or half-sib model).
The SAS code I have written to identify the lines of inheritance are far
from efficient and effective.  I would think matrix or vector is the way to
go, but I don't know SAS PROC IML well enough to do that nor do I have the
package on my machine.

Example :

Sire        m1    m2    n1    n2
100         1     2     1     2

Progeny     m1    m2    n1    n2
101         3     2     1     1

So the likely sire phase (gamete)  is 2 - 1 (m2 - n1).

I hope it helps.

Thanks again. Stella
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On Mon, 6 Dec 2004 13:36:37 +1300
ssim at lic.co.nz wrote:
> Dear lists,
> 
> I want to construct a loop in R, but don't know how to do it. I can do
it
> in SAS, but I prefer in R  (which I am hoping I will off SAS for good
> soon). Could anyone help me to convert the SAS codes to equivalent R codes.
> 
> Basically, the following codes were written to establish the sire gametes
> or phases for daughter design for one markers two alleles.
> 
> Here are the SAS code:
> 
You may try this code. There may be better code from others.

m<-array(0, 795) #phase
for ( i in 1:744) {  # sire
  for (j in 745:1540) { # progeny
    if (sire[j] == anim[i] ) {  #check if the progeny j is sired by animal i
      if (m1[j]==m1[i]  &&  m2[j]==m2[i] ) { m[j]=0; next}
      if ( m1[j]==m1[i]) { m[j] = 1; next}
      if (m1[j]==m2[i]) { m[j==2; next}
  
.....

    }
  }
}   



> do i=1 to 744;
>       do j=745 to 1540;
>             m[j]=0;
>             if sire[j]=anml[i] then do;
>                 if m1[j]=m1[i]  and m2[j]=m2[i] then m[j]=0;
>                 else if m1[j]=m1[i] then m[j] =1;
>                 else if m1[j]=m2[i] then m[j==2;
>                 else if m2[j]=m1[i] then m[j]=1;
>                 else if m2[j]=m2[i] then m[j]=2;
>                 else m[j]=0;
>             end do;
>      end;
> end;
> 
> 
> Thanks Stella
> ___________________________________________________________________________
> This message, including attachments, is confidential. If you...{{dropped}}
> 
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-- 

--
Yuandan Zhang, PhD

Animal Genetics and Breeding Unit
The University of New England
Armidale, NSW, Australia, 2351

E-mail:   yzhang4 at metz.une.edu.au
Phone:    (61) 02 6773 3786
Fax:      (61) 02 6773 3266
http://agbu.une.edu.au
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  AGBU is a joint venture of NSW Primary Industries 
  and The University of New England to undertake 
  genetic R&D for Australia's Livestock Industries           
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~