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 though of creating some fucntion to catch the error messages that
would otherwise scr*w things over:

my.lrm = function(x){
pol = NULL
pol = lrm( cpstc.f ~ x + time.cpstc + age + sex + mri)
if(length(pol) > 0)
rez = anova(pol)[1,3]
if(length(pol) ?== 0)
rez = 1
rez}

my.results = apply(chr, 2, my.lrm)

Still no joy, even adding try() in the evaluation and
options(show.error.messages = F)

I am at loss on how to get the darn function to bail out *silently* if needs
be so I can just smack a replacement value in --which would also have the
benefit of keeping the order of the markers.

Any idea will be gratefully acknowledged.

Best,

Federico


--
Federico C. F. Calboli
Department of Epidemiology and Public Health
Imperial College, St Mary's Campus
Norfolk Place, London W2 1PG

Tel ?+44 (0)20 7594 1602 ? ? Fax (+44) 020 7594 3193

f.calboli [.a.t] imperial.ac.uk
f.calboli [.a.t] gmail.com