## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>"
)
options(warn=-1)

## ---- eval=FALSE--------------------------------------------------------------
#  if (!requireNamespace("BiocManager", quietly=TRUE))
#      install.packages("BiocManager")
#  BiocManager::install("HiCDOC")

## -----------------------------------------------------------------------------
library(HiCDOC)

## ----tabFormat, eval = FALSE--------------------------------------------------
#  hic.experiment <- HiCDOCDataSetFromTabular('path/to/data.tsv')

## ----coolFormat, eval = FALSE-------------------------------------------------
#  # Path to each file
#  paths = c(
#      'path/to/condition-1.replicate-1.cool',
#      'path/to/condition-1.replicate-2.cool',
#      'path/to/condition-2.replicate-1.cool',
#      'path/to/condition-2.replicate-2.cool',
#      'path/to/condition-3.replicate-1.cool'
#  )
#  
#  # Replicate and condition of each file. Can be names instead of numbers.
#  replicates <- c(1, 2, 1, 2, 1)
#  conditions <- c(1, 1, 2, 2, 3)
#  
#  # Resolution to select in .mcool files
#  binSize = 500000
#  
#  # Instantiation of data set
#  hic.experiment <- HiCDOCDataSetFromCool(
#      paths,
#      replicates = replicates,
#      conditions = conditions,
#      binSize = binSize # Specified for .mcool files.
#  )

## ----hicFormat, eval = FALSE--------------------------------------------------
#  # Path to each file
#  paths = c(
#      'path/to/condition-1.replicate-1.hic',
#      'path/to/condition-1.replicate-2.hic',
#      'path/to/condition-2.replicate-1.hic',
#      'path/to/condition-2.replicate-2.hic',
#      'path/to/condition-3.replicate-1.hic'
#  )
#  
#  # Replicate and condition of each file. Can be names instead of numbers.
#  replicates <- c(1, 2, 1, 2, 1)
#  conditions <- c(1, 1, 2, 2, 3)
#  
#  # Resolution to select
#  binSize <- 500000
#  
#  # Instantiation of data set
#  hic.experiment <- HiCDOCDataSetFromHiC(
#      paths,
#      replicates = replicates,
#      conditions = conditions,
#      binSize = binSize
#  )

## ----hicproFormat, eval = FALSE-----------------------------------------------
#  # Path to each matrix file
#  matrixPaths = c(
#      'path/to/condition-1.replicate-1.matrix',
#      'path/to/condition-1.replicate-2.matrix',
#      'path/to/condition-2.replicate-1.matrix',
#      'path/to/condition-2.replicate-2.matrix',
#      'path/to/condition-3.replicate-1.matrix'
#  )
#  
#  # Path to each bed file
#  bedPaths = c(
#      'path/to/condition-1.replicate-1.bed',
#      'path/to/condition-1.replicate-2.bed',
#      'path/to/condition-2.replicate-1.bed',
#      'path/to/condition-2.replicate-2.bed',
#      'path/to/condition-3.replicate-1.bed'
#  )
#  
#  # Replicate and condition of each file. Can be names instead of numbers.
#  replicates <- c(1, 2, 1, 2, 1)
#  conditions <- c(1, 1, 2, 2, 3)
#  
#  # Instantiation of data set
#  hic.experiment <- HiCDOCDataSetFromHiCPro(
#      matrixPaths = matrixPaths,
#      bedPaths = bedPaths,
#      replicates = replicates,
#      conditions = conditions
#  )

## ----reloadExample------------------------------------------------------------
data(exampleHiCDOCDataSet)

## ----filterSmallChromosomes---------------------------------------------------
hic.experiment <- filterSmallChromosomes(exampleHiCDOCDataSet, threshold = 100)

## ----filterSparseReplicates---------------------------------------------------
hic.experiment <- filterSparseReplicates(hic.experiment, threshold = 0.3)

## ----filterWeakPositions------------------------------------------------------
hic.experiment <- filterWeakPositions(hic.experiment, threshold = 1)

## ----normalizeTechnicalBiases-------------------------------------------------
suppressWarnings(hic.experiment <- normalizeTechnicalBiases(hic.experiment))

## ----normalizeBiologicalBiases------------------------------------------------
hic.experiment <- normalizeBiologicalBiases(hic.experiment)

## ----normalizeDistanceEffect--------------------------------------------------
hic.experiment <- 
    normalizeDistanceEffect(hic.experiment, loessSampleSize = 20000)

## ----detectCompartments-------------------------------------------------------
hic.experiment <- detectCompartments(
    hic.experiment,
    kMeansDelta = 0.0001,
    kMeansIterations = 50,
    kMeansRestarts = 20
)

## ----plotInteractions---------------------------------------------------------
p <- plotInteractions(hic.experiment, chromosome = "Y")
p

## ----plotDistanceEffect-------------------------------------------------------
p <- plotDistanceEffect(hic.experiment)
p

## ----extractCompartments------------------------------------------------------
compartments(hic.experiment)

## ----extractConcordances------------------------------------------------------
concordances(hic.experiment)

## ----extractDifferences-------------------------------------------------------
differences(hic.experiment)

## ----plotCompartmentChanges---------------------------------------------------
p <- plotCompartmentChanges(hic.experiment, chromosome = "Y")
p

## ----plotConcordanceDifferences-----------------------------------------------
p <- plotConcordanceDifferences(hic.experiment)
p

## ----plotCentroids------------------------------------------------------------
p <- plotCentroids(hic.experiment, chromosome = "Y")
p

## ----plotSelfInteractionRatios------------------------------------------------
p <- plotSelfInteractionRatios(hic.experiment, chromosome = "Y")
p

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

