# 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))
```
