calcFisher: Apply Fishers exact test
In mknoll/cnAnalysis450k: Copy Number Analysis for 450k Illumina Methylation Arrays

Description Usage Arguments Value Examples

Calculates p values (Fishers exact test) for gain/loss and given group assignment

1	calcFisher(data, cluster, bin = TRUE)

`data`	previously created CN matrix
`cluster`	group assignent, same order as data columns
`bin`	Aggregate Fishers p.values to < 0.001, <0.01, <0.05, <0.1, >0.1

vector with all p-values

data <- data.frame(smp1=c(0,1,1,-1,0),
smp2=c(0,1,0,1,1),
smp3=c(1,1,0,0,0))
rownames(data) <- c("chr1:10000", "chr1:50000", 
"chr1:100000", "chr1:150000", "chr1:200000")
group <- c(1,2,2)
calcFisher(data,group,FALSE)
calcFisher(data,group,TRUE)