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

## ----example------------------------------------------------------------------
library(detectPanel)

set.seed(9)
n <- 36
p <- 12
y <- rep(c("Control", "Case"), each = n / 2)
counts <- matrix(
  rpois(p * n, 50), nrow = p,
  dimnames = list(paste0("m", seq_len(p)), paste0("s", seq_len(n)))
)
counts[1:3, y == "Case"] <- counts[1:3, y == "Case"] + 60
meta <- data.frame(group = y, row.names = colnames(counts))

fit <- discover_panel(
  counts, meta,
  outcome = "group",
  positive = "Case",
  candidate_n = 7,
  min_mean = 5,
  min_median = 2,
  min_detection = 0.3,
  min_group_detection = 0.2,
  min_auc = 0.55,
  outer_v = 3,
  outer_repeats = 1,
  inner_v = 3,
  inner_repeats = 1
)

fit$nested$outer_summary
fit$nested$feature_frequency