[R] Message for R-help mailing list

[Jeremy Miles]

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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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