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fisher.test(x)[1]
Jeremy
On 26 July 2011 14:51, Zmarz, Pawel <pawel.zmarz05 at imperial.ac.uk>
wrote:> Dear r-helpers,
>
> I would be very grateful if you could post the message below on the r-help
discussion board. Thank you very much!
>
> Best Wishes,
> Pawel
>
>
> Hello R community,
>
> I am generating lots of results using the fisher.test function, testing
many 2x2 tables of SNPs for association with a particular phenotype.
>
> A typical output of the fisher.test function would be (for example):
>
> data: ?data1
> p-value = 0.9837
> alternative hypothesis: true odds ratio is greater than 1
> 95 percent confidence interval:
> ?0.4162551 ? ? ? Inf
> sample estimates:
> odds ratio
> ?0.6262607
>
> That's lovely, but my problem is that I am only interested in the
"p-value" result for each SNP that I check. If it is possible, I would
like to extract all the p-values I generate (I use a loop to generate all of
them), chuck them into a matrix, and then into a text file. Or perhaps directly
export them into a text file, without using a matrix -- whatever is easier.
However, I am stuck on how to do this...
>
> Maybe one way would be to save the full results (as they are above) into a
text file and then get R to read just the specific part of the file (i.e. the
p-value part) and then build a matrix...but I do not know what the code would be
for the "specific reading" part..?
>
> Would anyone have any ideas??
>
> Thank you so much for your help!!!
>
> Best Wishes,
> Pawel
>
> ? ? ? ?[[alternative HTML version deleted]]
>
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