getDiffGenes: get differentially expressed genes in a data.frame

In rmflight/ccPaper: work for categoryCompare paper revisions

Description

get differentially expressed genes in a data.frame

Usage

  getDiffGenes(rankedData, id = "aggregateBy",
    useP = "adj.P.Val", pcutoff = 0.05, lfc = "logFC",
    lfcCutoff = NA, splitDir = TRUE)

Arguments

rankedData	data.frame of p-values and fold changes
id	the column to use as a returned id
useP	the column with the p-values
pcutoff	maximum p-value to use
lfc	column identifier for log-fold-change
lfcCutoff	should a minumum fold-change be required
splitDir	should significant results be split by up and down?

Details

if splitDir=TRUE (default), then the returned list will have up, dn, and universe. If splitDir=FALSE, then it will be sig and universe.

Value

list

rmflight/ccPaper documentation built on May 27, 2019, 9:31 a.m.