[R] Table of P values for Fisher's exact test

[Jacques VESLOT]

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)
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Jacques VESLOT

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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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