getDiffExpressedGenes: Perform differential gene expression analysis for mRNA...

In RTCGAToolbox: A new tool for exporting TCGA Firehose data

Description

getDiffExpressedGenes returns a list that stores the results for each dataset.

Usage

getDiffExpressedGenes(
  dataObject,
  DrawPlots = TRUE,
  adj.method = "BH",
  adj.pval = 0.05,
  raw.pval = 0.05,
  logFC = 2,
  hmTopUpN = 100,
  hmTopDownN = 100,
  meanFilter = 10
)

Arguments

dataObject	This must be FirehoseData object.
DrawPlots	A logical parameter to draw heatmaps and volcano plots.
adj.method	Raw p value adjustment methods (Default "BH")
adj.pval	Adjusted p value cut off for results table (Default 0.05)
raw.pval	raw p value cut off for results table (Default 0.05)
logFC	log fold change cut off for results table (Default 2)
hmTopUpN	Max number of up regulated genes in heatmap (Default 100)
hmTopDownN	Max number of down regulated genes in heatmap (Default 100)
meanFilter	Mean read counts for each gene to filter not expressed genes (Default 10)

Value

Returns a list that stores results for each dataset

Examples

data(accmini)

Example output

RTCGAToolbox documentation built on Nov. 8, 2020, 5:34 p.m.