getDiffGenes: get differentially expressed genes in a data.frame

Description Usage Arguments Details Value

View source: R/hypotheticalDataGeneration.R

Description

get differentially expressed genes in a data.frame

Usage

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  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 25, 2017, 4:26 a.m.