## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 7,
  fig.height = 5
)

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

## ----compPASS_score-----------------------------------------------------------
# Run CompPASS scoring
scoreCompPASS <- CompPASS(TestDatInput)

# View the top results
head(scoreCompPASS[order(scoreCompPASS$scoreWD, decreasing = TRUE), ])

## ----compPASS_plot, echo=TRUE-------------------------------------------------
par(mfrow = c(1, 1))
plot(sort(scoreCompPASS$scoreWD, decreasing = TRUE), 
     pch = 20, col = "royalblue",
     xlab = "Ranked Interactions", 
     ylab = "WD-score",
     main = "CompPASS WD-score Distribution")
abline(h = mean(scoreCompPASS$scoreWD) + 2 * sd(scoreCompPASS$scoreWD), 
       col = "red", lty = 2)
legend("topright", legend = "Mean + 2SD", col = "red", lty = 2)

## ----hg_score-----------------------------------------------------------------
# Run HG scoring
scoreHG <- HG(TestDatInput)

# View the top results
head(scoreHG[order(scoreHG$HG, decreasing = TRUE), ])

## ----hg_plot, echo=TRUE-------------------------------------------------------
plot(sort(scoreHG$HG, decreasing = TRUE), 
     pch = 20, col = "darkorange",
     xlab = "Ranked Interactions", 
     ylab = "HGscore",
     main = "HGScore Distribution")

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