chromophobe-package: Package to explore genomic enrichments for ChromHMM and...

In ttriche/chromophobe: Explore genomic state models, predictions, sample compositions & overlaps

Package to explore genomic enrichments for ChromHMM and related state models

Description

ChromHMM is a wonderful tool for heavy lifting and modeling chromatin states. As a post-processing tool it is slightly less wonderful, and if to plot how cell-type-specific changes fall into various states, it's a bit of a pain. This package makes it easier to relabel, prune/collapse, plot, and/or annotate the output of a ChromHMM run, runs, or other experiments mapped onto segments. Functions are also provided to ease compositional analysis of DNA methylation data (see ?composition), import/export segmentations (see ?bumps2bed), and various other conveniences often desired when working with these models.

Details

Package:	chromophobe
Type:	Package
Version:	0.1
Date:	2013-12-22
License:	APL

More here soon. This is a 0.1 release. Try import.ChromHMM(yourBedFile). See also ?composition and ?bumps2bed for some convenience functions.

Author(s)

Tim Triche, Jr. <[e-mail]>

References

ChromHMM: automating chromatin-state discovery and characterization Jason Ernst & Manolis Kellis

Examples

## not run:
## 
## bladder.HMM <- import.ChromHMM(
##   file="~/Dropbox/ChromHMM/RoadCODE3.model25/BLADDER_25_segments.bed", 
##   as='GRL', 
##   genome='hg19'
## )
##
## bladder <- import.posterior(
##   HMM=bladder.HMM, 
##   path="~/Dropbox/ChromHMM/RoadCODE3.model25/POSTERIOR",
##   states="~/Dropbox/ChromHMM/RoadCODE3.model25/labelStates.txt"
## )
## 
## plot.ChromHMM( 
##   bladder, 
##   what=c('genomic')
## )
## 

ttriche/chromophobe documentation built on Oct. 14, 2024, 11:59 a.m.