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

## ----load_data----------------------------------------------------------------
library(SMAD)
data("TestDatInput")
head(TestDatInput)

## ----compPASS-----------------------------------------------------------------
scoreCompPASS <- CompPASS(TestDatInput)
head(scoreCompPASS)

## ----HG-----------------------------------------------------------------------
scoreHG <- HG(TestDatInput)
head(scoreHG)

## ----DICE---------------------------------------------------------------------
scoreDICE <- DICE(TestDatInput)
head(scoreDICE)

## ----Hart---------------------------------------------------------------------
scoreHart <- Hart(TestDatInput)
head(scoreHart)

## ----PE-----------------------------------------------------------------------
# PE might require data.table and RcppAlgos
scorePE <- PE(TestDatInput)
head(scorePE)

## ----SAINT_spc----------------------------------------------------------------
# Using example data from the package
bait_path <- system.file("exdata", "TIP49", "bait.dat", package = "SMAD")
prey_path <- system.file("exdata", "TIP49", "prey.dat", package = "SMAD")
inter_path <- system.file("exdata", "TIP49", "inter.dat", package = "SMAD")

bait <- read.table(bait_path, sep = "\t", header = FALSE, 
                   col.names = c("ip_id", "bait_id", "test_ctrl"))
prey <- read.table(prey_path, sep = "\t", header = FALSE, 
                   col.names = c("prey_id", "prey_length"))
inter <- read.table(inter_path, sep = "\t", header = FALSE, 
                    col.names = c("ip_id", "bait_id", "prey_id", "quant"))

result_spc <- SAINTexpress_spc(inter, prey, bait)
head(result_spc[, c("Bait", "Prey", "SaintScore", "BFDR")])

## ----SAINT_int----------------------------------------------------------------
# Re-using the same example data for demonstration purposes
result_int <- SAINTexpress_int(inter, prey, bait)
head(result_int[, c("Bait", "Prey", "SaintScore", "BFDR")])

## ----visualization, fig.width=10, fig.height=6--------------------------------
par(mfrow = c(2, 3))
hist(scoreCompPASS$scoreWD, main = "CompPASS WD-score", xlab = "WD-score", col = "skyblue")
hist(scoreHG$HG, main = "HGScore", xlab = "HGScore", col = "salmon")
hist(scoreDICE$DICE, main = "DICE Score", xlab = "DICE", col = "lightgreen")
hist(scoreHart$Hart, main = "Hart Score", xlab = "Hart", col = "plum")
hist(scorePE$PE, main = "PE Score", xlab = "PE", col = "orange")
hist(result_spc$SaintScore, main = "SAINT Score (spc)", xlab = "SAINT Score", col = "gold")

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