[R] read table for Fisher Exact

Frank E Harrell Jr f.harrell at Vanderbilt.Edu
Thu May 13 14:35:07 CEST 2010

On 05/12/2010 03:31 PM, visser wrote:
> i have 2 groups i want to compare: group A and group B
> each group contains let's say 20 patients
> i want to perform a Fisher Exact test on genotype distribution
> so, see if there is a sign diff in genotpe frequency/distribution (#AA, #AB,
> #BB) between group A and B
> not for 1, but for 1000 different genes
> my question: how should i build my table so i can do:
> test<- read.table("table1.txt")
> fisher.test(test)
> i know a lot is still missing in the syntax, but i do not know what. any
> help would be soo much appreciated!!

Note that in this case, Fisher's exact test has a good chance of being 
less accurate than an approximate Pearson chi-square test.

Frank E Harrell Jr   Professor and Chairman        School of Medicine
                      Department of Biostatistics   Vanderbilt University

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