Null distribution histogram and statistic of the input set for enrichment analyses.

Description

Plots the distribution of gene set statistic values obtained in different resampling settings of an enrichment analysis, and draws the statistic value of the input set as a vertical line.

Usage

## S3 method for class 'gsaResult'
hist(x,
	signLevel = x$signLevel,
	subset = NULL,
	ask = FALSE,
	addLegend = TRUE,
	...)

Arguments

Details

The function plots the distribution of gene set statistic values under the null hypothesis. It requires the significance assessment step of the enrichment analysis configuration (parameter significance or gsAnalysis) to be a computer-intensive testing procedure that yields a distribution of gene set statistic p-values under the null hypothesis. Predefined configurations for which this plot works are analysis.gsea, analysis.averageCorrelation and analysis.averageTStatistic.

A histogram is plotted for the analysis in x. If x includes the analyses for several gene sets, one histogram is plotted for each of the gene sets.

The statistic value of the input set is depicted as a vertical line.

The most common graphical parameters can be supplied as vectors (one entry per analyzed gene set) to vary them between the different analyses. These parameters are: main, xlab, ylab.

See Also

geneSetAnalysis, predefinedAnalyses, gsAnalysis, evaluateGeneSetUncertainty, plot.uncertaintyResult

Examples

# load data
require(GlobalAncova)
data(vantVeer)
data(phenodata)
data(pathways)

res <- geneSetAnalysis(
	# global parameters
	dat = vantVeer,
	geneSets = pathways[3], 
	analysis = analysis.averageCorrelation(), 
	# additional parameters for analysis.averageCorrelation
	labs = phenodata$metastases,
	p = 1,
	numSamples = 100)

# plot the histogram for the cell cycle control gene set
hist(res, main = names(pathways[3]))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(GiANT)
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/GiANT/hist.Rd_%03d_medium.png", width=480, height=480)
> ### Name: hist
> ### Title: Null distribution histogram and statistic of the input set for
> ###   enrichment analyses.
> ### Aliases: hist.gsaResult
> 
> ### ** Examples
> 
> # load data
> require(GlobalAncova)
Loading required package: GlobalAncova
Loading required package: corpcor
Loading required package: globaltest
Loading required package: survival
> data(vantVeer)
> data(phenodata)
> data(pathways)
> 
> res <- geneSetAnalysis(
+ 	# global parameters
+ 	dat = vantVeer,
+ 	geneSets = pathways[3], 
+ 	analysis = analysis.averageCorrelation(), 
+ 	# additional parameters for analysis.averageCorrelation
+ 	labs = phenodata$metastases,
+ 	p = 1,
+ 	numSamples = 100)
> 
> # plot the histogram for the cell cycle control gene set
> hist(res, main = names(pathways[3]))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>