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cpsc
2009 Nov 10
1
when vectorising does not work: silent function fail?
Dear All,
I'm using apply to do some genetic association analysis along a chromosome, with
many thousands markers. For each marker the analysis is the same, so I was
planning to use apply(chrom, 2, somefunction)
In the specific case I do:
my.results = apply(chr, 2, function(x){anova(lrm( cpstc.f ~ x + time.cpstc + age
+ sex + mri))[1,3]})
This is all good and well in theory, but in practice the lrm() model will fail
for some markers and wreck the whole process. Failure for some markers is no
problem for me, but *predicting* which markers will fail can be hugely problematic.
I then t...