idsubset for qtscore

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Joined: Tue Feb 04, 2014 12:39 am

idsubset for qtscore

Postby thurlowl » Tue Feb 04, 2014 12:51 am

. I am trying to select a subset of my sheep Id’s for this particular GWAS but I can not get the subset function to work .

This is my code

Code: Select all

vec<-(phdata(df)$X1 == 1)
data2.qte <- qtscore(X.4, df,idsubset=vec, trait="gaussian")

I get this message in return

Code: Select all

Error: NAs in foreign function call (arg 7)

Phdata(df) is my dat file containing a list of id’s and phenotypes. Within this file I have SNPS list 1-15 and for each id they either have a 1 2 or 3 depending on the inheritance patterns of their alleles . for this instance above im just wanting to carry out GWAS on those that for SNP1 (X1) have a 1 which means they inherited their first allele from their sire and carry out a GWAS for trait (X.4) which is a meat trait (in millimeters) If you can help in any way please get back to me asap
Last edited by lckarssen on Tue Feb 04, 2014 10:51 am, edited 1 time in total.
Reason: Reformatted code with the [code] tag

Nicola Pirastu
GenABEL senior expert
GenABEL senior expert
Posts: 151
Joined: Wed Feb 09, 2011 3:24 pm

Re: idsubset for qtscore

Postby Nicola Pirastu » Sun Feb 09, 2014 8:29 am

If I understand correctly what you are trying to do, I think you should try something like:

Code: Select all

vec<-phdata(df)$id[which(phdata(df)$X1 == 1)]

There might be some NAs in $X1 which idsubset seems to not like very much.



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