## ----opts, eval = TRUE, echo=FALSE, results="hide", warning=FALSE------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", crop = NULL ) suppressPackageStartupMessages({ library(dplyr) library(GenomicRanges) library(HiContactsData) library(HiCExperiment) }) ## ----eval = FALSE------------------------------------------------------------- # if (!require("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("HiCExperiment") ## ----load_lib----------------------------------------------------------------- library(HiCExperiment) showClass("HiCExperiment") hic <- contacts_yeast() hic ## ----graph, eval = TRUE, echo=FALSE, out.width='100%'------------------------- knitr::include_graphics( "https://raw.githubusercontent.com/js2264/HiCExperiment/devel/man/figures/HiCExperiment_data-structure.png" ) ## ----import, eval = FALSE----------------------------------------------------- # hic <- import( # "path/to/contact_matrix.cool", # focus = "chr:start-end", # resolution = ... # ) ## ----evaled_import------------------------------------------------------------ library(HiContactsData) cool_file <- HiContactsData('yeast_wt', format = 'cool') import(cool_file, format = 'cool') ## ----many_imports------------------------------------------------------------- ## --- CoolFile pairs_file <- HiContactsData('yeast_wt', format = 'pairs.gz') coolf <- CoolFile(cool_file, pairsFile = pairs_file) coolf import(coolf) import(pairsFile(coolf), format = 'pairs') ## --- HicFile hic_file <- HiContactsData('yeast_wt', format = 'hic') hicf <- HicFile(hic_file, pairsFile = pairs_file) hicf import(hicf) ## --- HicproFile hicpro_matrix_file <- HiContactsData('yeast_wt', format = 'hicpro_matrix') hicpro_regions_file <- HiContactsData('yeast_wt', format = 'hicpro_bed') hicprof <- HicproFile(hicpro_matrix_file, bed = hicpro_regions_file) hicprof import(hicprof) ## ----focus-------------------------------------------------------------------- availableChromosomes(cool_file) hic <- import(cool_file, format = 'cool', focus = 'I:20001-80000') hic focus(hic) ## ----asym--------------------------------------------------------------------- hic <- import(cool_file, format = 'cool', focus = 'II:1-500000|II:100001-300000') focus(hic) ## ----mcool-------------------------------------------------------------------- mcool_file <- HiContactsData('yeast_wt', format = 'mcool') availableResolutions(mcool_file) availableChromosomes(mcool_file) hic <- import(mcool_file, format = 'cool', focus = 'II:1-800000', resolution = 2000) hic ## ----slots-------------------------------------------------------------------- fileName(hic) focus(hic) resolutions(hic) resolution(hic) interactions(hic) scores(hic) tail(scores(hic, 1)) tail(scores(hic, 'balanced')) topologicalFeatures(hic) pairsFile(hic) metadata(hic) ## ----extra-------------------------------------------------------------------- seqinfo(hic) ## To recover the `Seqinfo` object from the `.(m)cool` file bins(hic) ## To bin the genome at the current resolution regions(hic) ## To extract unique regions of the contact matrix anchors(hic) ## To extract "first" and "second" anchors for each interaction ## ----scores------------------------------------------------------------------- scores(hic, 'random') <- runif(length(hic)) scores(hic) tail(scores(hic, 'random')) ## ----features----------------------------------------------------------------- topologicalFeatures(hic, 'viewpoints') <- GRanges("II:300001-320000") topologicalFeatures(hic) topologicalFeatures(hic, 'viewpoints') ## ----as----------------------------------------------------------------------- as(hic, "GInteractions") as(hic, "ContactMatrix") as(hic, "matrix")[1:10, 1:10] as(hic, "data.frame")[1:10, ] ## ----pairs-------------------------------------------------------------------- import(pairs_file, format = 'pairs') ## ----session------------------------------------------------------------------ sessionInfo()