## ----small-cohort-setup, include = FALSE--------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")

## ----build-signature, warning = TRUE------------------------------------------
library(rnaSentry)
library(SummarizedExperiment)

set.seed(30)
n_sm <- 30
counts <- matrix(rpois(60 * n_sm, lambda = 500), nrow = 60, ncol = n_sm,
                 dimnames = list(paste0("gene", 1:60), paste0("S", 1:n_sm)))
sig_expr <- colMeans(counts[1:5, , drop = FALSE])
risk <- scale(sig_expr)[, 1] * 0.5
event_time <- rexp(n_sm, rate = 0.05 * exp(0.9 * risk))
censor_time <- rexp(n_sm, rate = 0.02)
cd <- S4Vectors::DataFrame(time = pmin(event_time, censor_time),
                           event = as.integer(event_time < censor_time),
                           row.names = colnames(counts))
se <- SummarizedExperiment(assays = list(counts = counts), colData = cd)

sig <- build_signature(se, "time", "event", top_n = 5,
                       repeats = 5, folds = 5, seed = 30)

## ----naive-summary------------------------------------------------------------
sig$cv_summary

## ----guardrail-flags----------------------------------------------------------
sig$flags

## ----per-fold-results---------------------------------------------------------
sig$cv_results

## ----small-fold-spread, fig.width = 7, fig.height = 5, fig.align = "center", fig.cap = "Per-fold cross-validated concordance across repeats and folds (one point per fold). The vertical dashed line marks the mean; the spread from 0.50 to 1.00 is the instability the mean hides."----
set.seed(30)
cv <- sig$cv_results
stripchart(cv$c_index, method = "jitter", jitter = 0.12, pch = 19, cex = 1.1,
           ylim = c(0, 1.05), ylab = "Cross-validated C-index (per fold)",
           main = sprintf("Per-fold C-index: mean %.2f, sd %.2f",
                          mean(cv$c_index), stats::sd(cv$c_index)))
abline(v = mean(cv$c_index), lty = 2, col = "grey40")

## ----session-info-------------------------------------------------------------
sessionInfo()