inst/doc/hicClust.R

In adjclust: Adjacency-Constrained Clustering of a Block-Diagonal Similarity Matrix

## ----skipNoHITC---------------------------------------------------------------
# IMPORTANT: this vignette can not be created if HiTC is not installed
if (!require("HiTC", quietly = TRUE)) {
  knitr::opts_chunk$set(eval = FALSE)
}

## ----loadLib, message=FALSE---------------------------------------------------
library("adjclust")

## ----loadData-----------------------------------------------------------------
load(system.file("extdata", "hic_imr90_40_XX.rda", package = "adjclust"))

## ----create-data-script-------------------------------------------------------
system.file("system/create_hic_chrXchrX.R", package="adjclust")

## ----mapHiC, message=FALSE----------------------------------------------------
HiTC::mapC(hic_imr90_40_XX)

## ----hicClust-HTCexp, message=FALSE-------------------------------------------
fit <- hicClust(hic_imr90_40_XX)

## ----binning, message=FALSE---------------------------------------------------
binned <- HiTC::binningC(hic_imr90_40_XX, binsize = 1e5)
fitB <- hicClust(binned)
fitB

## ----plotBinned, message=FALSE------------------------------------------------
HiTC::mapC(binned)

## ----dendro-------------------------------------------------------------------
plot(fitB, mode = "corrected")

## ----objectDesc---------------------------------------------------------------
head(cbind(fitB$merge, fitB$gains))

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