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

## ----matrix-example-----------------------------------------------------------
set.seed(42)
counts <- matrix(rpois(30 * 8, lambda = 10), nrow = 30, ncol = 8)
rownames(counts) <- paste0("Taxon_", seq_len(30))
colnames(counts) <- paste0("Sample_", seq_len(8))

# Plant a signal: raise one set's members in the last four samples
counts[1:6, 5:8] <- counts[1:6, 5:8] * 5

my_sets <- list(
  elevated_set = paste0("Taxon_", 1:6),
  control_set  = paste0("Taxon_", 20:27)
)

scores <- ssTaxSEA(counts, custom_db = my_sets, min_set_size = 3)
dim(scores)
round(scores, 2)

## ----matrix-signal------------------------------------------------------------
rowMeans(scores[, 5:8]) - rowMeans(scores[, 1:4])

## ----single-sample------------------------------------------------------------
ssTaxSEA(counts[, 1, drop = FALSE], custom_db = my_sets, min_set_size = 3)

## ----builtin, eval = FALSE----------------------------------------------------
# scores <- ssTaxSEA(counts)
# dim(scores)

## ----tse, message = FALSE, eval = requireNamespace("SummarizedExperiment", quietly = TRUE)----
library(SummarizedExperiment)

se <- SummarizedExperiment(assays = list(counts = counts))
scores_se <- ssTaxSEA(se, custom_db = my_sets, min_set_size = 3)

# Identical to the matrix result
all.equal(scores, scores_se)

## ----baselines----------------------------------------------------------------
rowMeans(scores)

## ----centering----------------------------------------------------------------
scaled <- t(scale(t(scores)))
round(scaled, 2)

## ----testing------------------------------------------------------------------
group <- rep(c("control", "case"), each = 4)
wilcox.test(scores["elevated_set", ] ~ group)$p.value

## ----pseudocount--------------------------------------------------------------
p1 <- ssTaxSEA(counts, custom_db = my_sets, min_set_size = 3, pseudocount = 1)
round(p1["elevated_set", ] - scores["elevated_set", ], 3)

## ----sessioninfo--------------------------------------------------------------
sessionInfo()