TCGAbiolinks (version 1.0.10)

TCGAvisualize_EAbarplot: barPlot for a complete Enrichment Analysis

Description

TCGAvisualize_EAbarplot plots the result from TCGAanalyze_EAcomplete in a complete barPlot

Usage

TCGAvisualize_EAbarplot(tf, GOMFTab, GOBPTab, GOCCTab, PathTab, nBar, nRGTab)

Arguments

tf

is a list of gene symbols

GOMFTab

is results from TCGAanalyze_EAcomplete related to Molecular Function (MF)

GOBPTab

is results from TCGAanalyze_EAcomplete related to Biological Process (BP)

GOCCTab

is results from TCGAanalyze_EAcomplete related to Cellular Component (CC)

PathTab

is results from TCGAanalyze_EAcomplete related to Pathways EA

nBar

is the number of bar histogram selected to show (default = 10)

nRGTab

is the gene signature list with gene symbols.

Value

Complete barPlot from Enrichment Analysis showing significant (default FDR < 0.01) BP,CC,MF and pathways enriched by list of genes.

Examples

Genelist <- c("FN1","COL1A1")
ansEA <- TCGAanalyze_EAcomplete(TFname="DEA genes Normal Vs Tumor",Genelist)
TCGAvisualize_EAbarplot(tf = rownames(ansEA$ResBP),
         GOBPTab = ansEA$ResBP,
         GOCCTab = ansEA$ResCC,
         GOMFTab = ansEA$ResMF,
        PathTab = ansEA$ResPat,
         nRGTab = Genelist,
         nBar = 10)
## Not run: 
# Genelist <- rownames(dataDEGsFiltLevel)
# system.time(ansEA <- TCGAanalyze_EAcomplete(TFname="DEA genes Normal Vs Tumor",Genelist))
# # Enrichment Analysis EA (TCGAVisualize)
# # Gene Ontology (GO) and Pathway enrichment barPlot
# TCGAvisualize_EAbarplot(tf = rownames(ansEA$ResBP),
#          GOBPTab = ansEA$ResBP,
#          GOCCTab = ansEA$ResCC,
#          GOMFTab = ansEA$ResMF,
#         PathTab = ansEA$ResPat,
#          nRGTab = Genelist,
#          nBar = 10)
# ## End(Not run)