This is clearly a message for the R-help mailing list, since it was sent to the R help mailing list.
fisher.test(x)[1] Jeremy On 26 July 2011 14:51, Zmarz, Pawel <pawel.zmar...@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]] > > ______________________________________________ > 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. > ______________________________________________ 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.
