On 27.07.2011 02:17, Jeremy Miles wrote:
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]
Since the test object is actually a list, your probably want fisher.test(x)[[1]] or more obvious fisher.test(x)[["p.value"]] Uwe Ligges
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.
______________________________________________ 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.
