apply(yourdata[, c("X2N_CHB","X2N_AA","Counts_CHB","Counts_AA")], 1,
function(x)
fisher.test(cbind(x[3:4], x[1:2]-x[3:4]))$p.value)
-------------------------------------------------------------------
Jacques VESLOT
CNRS UMR 8090
I.B.L (2ème étage)
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59019 Lille Cedex
Tel : 33 (0)3.20.87.10.44
Fax : 33 (0)3.20.87.10.31
http://www-good.ibl.fr
-------------------------------------------------------------------
jenny tan a écrit :
> Hi,
>
> I have a table of observed counts for various genetic markers. Instead of
> doing Fisher's exact test for each marker one at a time and recording the P
> value manually, is there a script to go through the whole list and generate
> the P value column automatically?
>
> An example of my data:
>
>
> Counts_CHB and Counts_AA are the observed counts for one allele.
> 2N_CHB and 2N_AA are the total number of alleles.
>
> gene Local_Pos 2N_CHB 2N_AA Counts_CHB Counts_AA Exact_P
> B2M 2475 90 46 0 5
> B2M 3532 90 44 0 1
> FCN2 2203 88 46 0 1
> FCN2 3536 90 46 0 9
> FCN2 4027 84 46 0 9
> FCN2 4036 90 46 0 9
> FCN2 4318 90 46 0 9
> FCN2 4392 90 46 0 9
> FCN2 9575 90 46 0 1
>
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