| tnsSRD,TNS-method {RTNsurvival} | R Documentation |
This regulon evaluates differences between regulon activity of subgroups of samples, given a grouping variable. It performs Wilcoxon-Mann-Whitney (2 subgroups) or Kruskal-Wallis (3+ subgroups) Rank Sum Tests to check whether the activity scores of a given regulon are different between subgroups of samples.
## S4 method for signature 'TNS' tnsSRD(tns, subgroup, pValueCutoff = 0.05, pAdjustMethod = "BH", regs = NULL, verbose = TRUE)
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. |
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). |
regs |
An optional string vector specifying regulons to use for the analysis. |
verbose |
a logical value specifying whether to display messages and progress bar. |
A TNS-class object with the results of the subgroup regulon difference added to the results slot. To recover the results, use tnsGet(tns, "regulonDifference")
# 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 <- tnsSRD(stns, "ER+")