disco (version 0.6)

percentGenes: Calculates percentage of present genes from a specified superset of expression modules

Description

This function counts the number of genes in modules specified in data.frame created by tmodCERNOtest function and returns percentage of those genes which are present in data.frame on the basis of which the enrichment was calculated, as well as original number of genes present in the module.

Usage

percentGenes(orthologs, mset = NULL)

Arguments

orthologs

object of class matchedOrtholog

mset

a tmod module set (object of class tmod). If NULL, the default tmod object will be used.

Value

data frame with columns specifying percentages of genes present in subsequent modules "p_genes" and the overall amount of genes in the modules "all_genes"

Examples

# NOT RUN {
library(tmod)
data(tmod)
data(orthologs)
disco <- disco.score(orthologs)
ord <- order(disco, decreasing = TRUE)
concordant <- tmodCERNOtest(toupper(orthologs$genes)[ord])
modtable <- percentGenes(orthologs, tmod[concordant$ID])
cbind(concordant, modtable)
# }