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