tnsPlotGSEA2,TNS-method {RTNsurvival} | R Documentation |
Makes a 2-tailed GSEA plot for a certain phenotype (sample)
present in a TNS. A wrapper of tna.plot.gsea2
## 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, ... )
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 |
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 |
A plot containing the 2-tailed GSEA analysis for a phenotype.
tna.plot.gsea2
for all plot parameters
# 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)