percentGenes: Calculates percentage of present genes from a specified...

In disco: Discordance and Concordance of Transcriptomic Responses

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

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)

disco documentation built on May 2, 2019, 9:40 a.m.