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
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