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-% Generated by roxygen2: do not edit by hand
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-% Please edit documentation in R/importOtherSegmentations.R
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-\name{importChromHMMsegmentation}
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-\alias{importChromHMMsegmentation}
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-\title{Import ChromHMM segmentation}
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-\usage{
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-importChromHMMsegmentation(inputfolder, outputfolder, assembly, binsize,
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- experiment.table, chrom.lengths = NULL, chromosomes = NULL,
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- chromosome.format = "UCSC")
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-}
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-\arguments{
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-\item{inputfolder}{Folder with ChromHMM output files (segmentation, emission and transition probabilities).}
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-
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-\item{outputfolder}{Output folder for the converted \code{\link{chromstaR-objects}}.}
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-
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-\item{assembly}{An assembly from which the chromosome lengths are determined. Please see \code{\link[GenomeInfoDb]{fetchExtendedChromInfoFromUCSC}} for available assemblies. Alternatively a data.frame generated by \code{\link[GenomeInfoDb]{fetchExtendedChromInfoFromUCSC}}.}
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-
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-\item{binsize}{The bin size in base pairs used in ChromHMM.}
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-
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-\item{experiment.table}{A \code{data.frame} or tab-separated text file with the structure of the experiment. See \code{\link{experiment.table}} for an example.}
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-
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-\item{chrom.lengths}{A named character vector with chromosome lengths. Names correspond to chromosomes.}
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-
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-\item{chromosomes}{A subset of chromosomes for which the bins are generated.}
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-
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-\item{chromosome.format}{A character specifying the format of the chromosomes if \code{assembly} is specified. Either 'NCBI' for (1,2,3 ...) or 'UCSC' for (chr1,chr2,chr3 ...).}
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-}
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-\value{
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-A \code{\link{combinedMultiHMM}} object. Intermediate \code{\link{multiHMM}} objects are saved to \code{outputfolder}.
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-}
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-\description{
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-Import a chromatin state segmentation produced by ChromHMM as \code{\link{chromstaR-objects}}. This is useful to perform comparative analyses or simply use chromstaR plotting or enrichment functions on a ChromHMM segmentation.
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-}
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-\details{
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-The function takes the *segments.bed files, emissions_*.txt and transitions_*.txt files in \code{inputfolder}, and converts them into \code{\link{multiHMM}} objects for each condition that was specified in the \code{experiment.table}. All \code{\link{multiHMM}} objects are then combined into a \code{\link{combinedMultiHMM}} object and returned.
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-}
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-\examples{
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-inputfolder <- "differential_CD4_numstates_16_binsize_1000bp"
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-outputfolder <- "testconvertChromHMM2chromstar"
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-assembly <- "mm9"
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-binsize <- 1000
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-chrom.lengths <- NULL
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-chromosomes <- paste0("chr", c(1:19, "X"))
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-chromosome.format <- "UCSC"
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-experiment.table <- "differential_CD4_numstates_16_binsize_1000bp/experiment_table_differential_CD4.tsv"
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-model <- importChromHMMsegmentation(inputfolder, outputfolder, assembly, binsize, experiment.table, chrom.lengths, chromosomes, chromosome.format)
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-
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-### Plot transition and emission probabilities of ChromHMM model ###
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-heatmapTransitionProbs(reorder.states=FALSE, transitionProbs=model$transitionProbs)
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-heatmapCombinations(emissionProbs = model$emissionProbs)
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-
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-### Use plotEnrichment function on imported ChromHMM segmentation ###
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-library(biomaRt)
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-ensembl <- useMart('ENSEMBL_MART_ENSEMBL', host='may2012.archive.ensembl.org',
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- dataset='mmusculus_gene_ensembl')
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-genes <- getBM(attributes=c('ensembl_gene_id', 'chromosome_name', 'start_position',
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- 'end_position', 'strand', 'external_gene_id',
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- 'gene_biotype'),
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- mart=ensembl)
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-# Transform to GRanges for easier handling
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-genes <- GRanges(seqnames=paste0('chr',genes$chromosome_name),
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- ranges=IRanges(start=genes$start, end=genes$end),
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- strand=genes$strand,
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- name=genes$external_gene_id, biotype=genes$gene_biotype)
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-print(genes)
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-
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-ggplts <- plotEnrichment(model, annotation=genes)
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-ggplts[[1]] + facet_wrap(~combination)
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-
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-}
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