DPA: DPA

In ibsquare/MoonlightR: Identify oncogenes and tumor suppressor genes from omics data

DPA

Description

This function carries out the differential phenotypes analysis

Usage

DPA(
  dataType,
  dataFilt,
  dataConsortium = "TCGA",
  fdr.cut = 0.01,
  logFC.cut = 1,
  diffmean.cut = 0.25,
  samplesType,
  colDescription,
  gset,
  gsetFile = "gsetFile.RData"
)

Arguments

dataType	selected
dataFilt	obtained from getDataTCGA
dataConsortium	is TCGA or GEO, default TCGA
fdr.cut	is a threshold to filter DEGs according their p-value corrected
logFC.cut	is a threshold to filter DEGs according their logFC
diffmean.cut	diffmean.cut for DMR
samplesType	samplesType
colDescription	colDescription
gset	gset
gsetFile	gsetFile

Value

result matrix from differential phenotype analysis

Examples

dataDEGs <- DPA(dataFilt = dataFilt, dataType = "Gene expression")

ibsquare/MoonlightR documentation built on May 19, 2024, 6:16 a.m.