tnsPlotGSEA2-methods: Plot 2-tailed GSEA for a sample from a TNS

In csgroen/RTNsurvival: Survival analysis using transcriptional networks inferred by the RTN package

Description

Makes a 2-tailed GSEA plot for a certain phenotype (sample) present in a TNS. A wrapper of tna.plot.gsea2

Usage

## S4 method for signature 'TNS'
tnsPlotGSEA2(tns, aSample, regs = NULL, refsamp = NULL,
  checklog = FALSE, ntop = NULL, pValueCutoff = 0.05,
  pAdjustMethod = "BH", verbose = TRUE, plotpdf = FALSE, ...)

Arguments

tns	A TNS object
aSample	A string specifying a given sample number present in the 'survivalData' table.
regs	An optional string vector specifying regulons to make the plot.
refsamp	A character vector.
checklog	A logical value. If TRUE, expression values are transformed into log space.
ntop	An optional integer value. The number of regulons for which the GSEA2 will be plotted.
pValueCutoff	An numeric value. The p-value cutoff for the analysis.
pAdjustMethod	A character. Specifies the adjustment method for the pvalue. See p.adjust
verbose	A logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE).
plotpdf	A single logical value.
...	parameters which will be passed to tna.plot.gsea2, such as ylimPanels, heightPanels, width, height, ylabPanels, xlab...

Value

A plot containing the 2-tailed GSEA analysis for a phenotype.

See Also

tna.plot.gsea2 for all plot parameters

Examples

# load survival data
data(survival.data)

# load TNI-object
data(stni, package = "RTN")

stns <- tni2tnsPreprocess(stni, survivalData = survival.data, 
        keycovar = c('Grade','Age'), time = 1, event = 2)
stns <- tnsGSEA2(stns, verbose=FALSE)
tnsPlotGSEA2(stns, 'MB-5115', regs = 'FOXM1', plotpdf = FALSE)

csgroen/RTNsurvival documentation built on May 20, 2019, 1:49 p.m.