On 10 Nov 2009, at 17:16, tlum...@u.washington.edu wrote:
On Tue, 10 Nov 2009, jim holtman wrote:
Have you tried something like this:
my.results = apply(chr, 2, function(x){
result <- try(anova(lrm( cpstc.f ~ x + time.cpstc + age + sex +
mri))[1,3])
if (inherits(result, "try-error")) return(NULL)
result
})
This should catch the error and have NULL in that list element.
It's probably more useful to return a numeric vector of the right
size, with tryCatch()
tryCatch(anova(lrm( cpstc.f ~ x + time.cpstc + age + sex + mri))
[1,3],
error=function(e) NA)
Both suggestions work beautifully, thanks to both!
Also, you probably get less data copying by using a for() or while()
loop than by using apply() in this context.
I'm happy to take this in, I am not sure I can see how it would work
(the less data copying) though.
Finally, the overhead of formula parsing and model matrix
construction repeated thousands of times probably dominates this
computation; if it isn't just a one-off it would probably be worth a
lower-level implementation.
The markers are ~ 1.5M, but I don't do this kind of analysis often
enough to justify any more work than a measly script.
Cheers,
Fede
-thomas
On Tue, Nov 10, 2009 at 10:04 AM, Federico Calboli
<f.calb...@imperial.ac.uk> wrote:
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
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
______________________________________________
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Thomas Lumley Assoc. Professor, Biostatistics
tlum...@u.washington.edu University of Washington, Seattle
--
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 75941602 Fax +44 (0)20 75943193
f.calboli [.a.t] imperial.ac.uk
f.calboli [.a.t] gmail.com
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
