tnsSRE,TNS-method {RTNsurvival} | R Documentation |
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.
## S4 method for signature 'TNS' tnsSRE(tns, subgroup, regs = NULL, pValueCutoff = 0.05, pAdjustMethod = "BH")
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). |
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")
# 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)