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README.md
![Basic Checks](https://github.com/MahShaaban/segmenter/workflows/Basic%20Checks/badge.svg) ![Build and Push Docker Image](https://github.com/MahShaaban/segmenter/workflows/Build%20and%20Push%20Docker%20Image/badge.svg) # segmenter Perform Chromatin Segmentation Analysis in R by Calling ChromHMM ## Description Call *chromHMM* from within *R*, capture the output files in an `S4` object and interface to other relevant Bioconductor analysis tools. In addition `segmenter` provides functions to test, select and visualize the output of the segmentation. ## Installation You can install the released version of `segmenter` from [Bioconductor](https://bioconductor.org/) with: ``` r BiocManager::install("segmenter") ``` or the development version from GitHub with: ```r remotes::install_github('MahShaaban/segmenter@devel') ``` ## Getting started ```r # load required libraries library(segmenter) ``` ```r # locate input and annotation files inputdir <- system.file('extdata/SAMPLEDATA_HG18', package = 'segmenter') coordsdir <- system.file('extdata/COORDS', package = 'chromhmmData') anchorsdir <- system.file('extdata/ANCHORFILES', package = 'chromhmmData') chromsizefile <- system.file('extdata/CHROMSIZES', 'hg18.txt', package = 'chromhmmData') ``` ```r # run command obj <- learn_model(inputdir = inputdir, coordsdir = coordsdir, anchorsdir = anchorsdir, chromsizefile = chromsizefile, numstates = 3, assembly = 'hg18', cells = c('K562', 'GM12878'), annotation = 'RefSeq', binsize = 200) ``` ```r # show the object show(obj) ``` ```r # access object slots emission(obj) ``` ```r # operate on the object get_frequency(segments = segment(obj)) ```