R/runFisher2sided.R

In montilab/K2Taxonomer: Creating annotated submodules of high-throughput data through recursive partitioning

## Create data.frame of factor variable
.runFisher2sided <- function(csDF) {

    ## Run test
    if (sum(!is.na(csDF$value[csDF$cat])) > 0 &
        sum(!is.na(csDF$value[!csDF$cat])) > 0) {
        fisherOut <- fisher.test(csDF$cat, csDF$value, simulate.p.value=TRUE)
        pval <- fisherOut$p.value
        stat <- fisherOut$estimate
    } else {
        pval <- NA
        stat <- NA
    }

    if (is.null(stat)) {
        stat <- NA
    }

    ## Generate results
    data.frame(pval=pval, stat=stat, df=NA, obsMean=NA,
        altMean=NA, diffMean=NA, nhits=NA, ncase=NA,
        nalt=NA, ndrawn=NA, hits=NA, test="two-sided Fishers Exact Test",
        stringsAsFactors=FALSE)
}