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

## ----install, eval=FALSE------------------------------------------------------
# BiocManager::install("fourSynergy")

## ----libs, message=FALSE------------------------------------------------------
library(fourSynergy)

## ----data, eval=TRUE----------------------------------------------------------
# Load config
config <- system.file("extdata", "Datasets", "Demo", "info.yaml",
    package = "fourSynergy"
)

# Load results path
res_path <- system.file("extdata", "results", "Demo",
    package = "fourSynergy"
)

# Load path of .bedGraphs
tracks <- system.file("extdata", "results", "Demo", "alignment",
    package = "fourSynergy"
)
sia <- createIa(
    res_path = res_path,
    config = config,
    tracks = tracks
)

## ----slots, eval=TRUE---------------------------------------------------------
slotNames(sia)

## ----plot_ia, message=FALSE, eval=TRUE, warning=FALSE-------------------------
plotIaIndiviualTools(sia, genes_of_interest = c("Ldlrad4", "Cep76"))

## ----plot_tracks_base, message=FALSE, eval=TRUE, warning=FALSE----------------
plotBaseTracks(sia)

## ----ens----------------------------------------------------------------------
sia <- consensusIa(sia, model = "AUPRC")

## ----plot_ens, warning=FALSE--------------------------------------------------
plotConsensusIa(ia = sia)

## ----plot_ens_tracks, message=FALSE, eval=TRUE, warning=FALSE-----------------
plotConsensusTracks(sia)

## ----diff---------------------------------------------------------------------
sia <- differentialAnalysis(ia = sia, fitType = "mean")

## ----diffplot, message=FALSE--------------------------------------------------
plotDiffIa(ia = sia, genes_of_interest = c("Ldlrad4", "Cep76"))

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