CODEWITHSUNDEEP
r
user12
user12

Reputation: 91

Fisher exact test for each gene

I would like to do rna seq data for several genes, tested in control and treatment. To do fisher.test I need a contingency table for each gene, is there a way to do this in R instead of computing a contingency table for each gene? I am new to this so any advice can be helpful.

I have the count data and the sample Info data,

                control1 treated1 control2 treat2 control3 treat3
ENSG00000000003        723        486        904        445       1170       1097  
ENSG00000000005          0          0          0          0          0          0 
ENSG00000000419        467        523        616        371        582        781

Where ENSG are the genes

Upvotes: 0

Views: 415

Answers (1)

Ben Bolker
Ben Bolker

Reputation: 226911

Reading in your data:

dd <- read.table(header=TRUE,text="
              control1 treated1 control2 treat2 control3 treat3
ENSG00000000003        723        486        904        445       1170       1097  
ENSG00000000005          0          0          0          0          0          0 
ENSG00000000419        467        523        616        371        582        781 
")

Running a for loop, with some safeguards:

results <- list()
for (i in 1:nrow(dd)) {
    m <- matrix(unlist(dd[i,]),nrow=2)
    if (any(m>0)) {
       results[[i]] <- fisher.test(m)
    } else {
        results[[i]] <- NA
    }
}
names(results) <- rownames(dd)

Upvotes: 1

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