simplifyHMM.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/simplifyHMM.R
\name{simplifyHMM}
\alias{simplifyHMM}
\title{convenience function for adding simplified names & colors to a ChromHMM track}
\usage{
simplifyHMM(HMM, cols = NULL, how = c("MNEMONIC", "STATE", "NUMBER"))
}
\arguments{
\item{HMM}{a GRanges containing a ChromHMM track}

\item{cols}{color table (will be loaded if not provided)}

\item{how}{one of `MNEMONIC` (default), `STATE`, or `NUMBER`}
}
\value{
the same ChromHMM track, but simplified and colored simply
}
\description{
convenience function for adding simplified names & colors to a ChromHMM track
}
\details{
if simplifying further than 5-6 states, fix the map first
}
\examples{

# simpler even than the defaults:
data(remc18state, package="chromophobe")
simpler <- remc18state
simpler$SIMPLE <- sub("(Promoter|Enhancer)", "Active", simpler$SIMPLE)
simpler$SIMPLE <- sub("(Transcribed|Het_Rpt_Qui)", "Other", simpler$SIMPLE)
simpler[simpler$SIMPLE == "Other", "RGBSIMPLE"] <- "255,255,255"

data(chr19_HMM, package="chromophobe")
simplerHMM <- simplifyHMM(chr19_HMM, cols=simpler)
with(simplerHMM, table(name))

# blueprint HMM simplification (better to use hg38, though)
\dontrun{
  data(FDFT1)
  bpHMMfiles <- list.files(patt="BlueprintChromHMM.*hg19.bed.gz$")
  names(bpHMMfiles) <- sapply(strsplit(bpHMMfiles,"\\\\."),`[`,1)
  bpHMMs <- GRangesList(lapply(bpHMMfiles, import, which=FDFT1))
  data(blueprint12state)
  simplified <- GRangesList(lapply(bpHMMs, simplifyHMM,
                                   cols=blueprint12state, how="NUMBER"))
  genome(simplified) <- "hg19"
  for (i in names(simplified)) compressAndExportHMM(simplified[[i]], i)
}

}
\references{
http://compbio.mit.edu/ChromHMM/
}
\seealso{
colorHMM
}