tnsSRE-methods: Subgroup Regulon Enrichment for TNS-class objects

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

Description

This method evaluates which regulons are enriched in sample groups, given a grouping variable. It performs Fisher's Exact Test whether a regulon is positively or negatively enriched in a subgroup using regulon activity.

Usage

## S4 method for signature 'TNS'
tnsSRE(tns, subgroup, regs = NULL, pValueCutoff = 0.05, pAdjustMethod = "BH")

Arguments

tns	A A TNS object.
subgroup	a character vector. It must be the name of a column in the survivalData featuring the grouping information as a categorical variable.
regs	An optional string vector specifying regulons to use for the analysis.
pValueCutoff	a single numeric value specifying the cutoff for p-values considered significant.
pAdjustMethod	a single character value specifying the p-value adjustment method to be used (see 'p.adjust' for details).

Value

A TNS-class object with the results of the subgroup regulon enrichment added to the results slot. To recover the results, use tnsGet(tns, "regulonEnrichment")

Examples

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

# create TNS object
stns <- tni2tnsPreprocess(stni, survivalData = survival.data,
                          keycovar = c('Grade','Age'), time = 1, event = 2)
stns <- tnsGSEA2(stns)

# run subgroup regulon enrichment analysis
stns <- tnsSRE(stns, "ER+")

# plot the result
tnsPlotSRE(stns)

RTNsurvival documentation built on Nov. 12, 2020, 2 a.m.