GRO-seq Analysis Pipeline


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Documentation for package ‘groHMM’ version 1.28.0

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groHMM-package groHMM: GRO-seq Analysis Pipeline
averagePlot Returns the average profile of tiling array probe intensity values or wiggle-like count data centered on a set of genomic positions (specified by 'Peaks').
breakTranscriptsOnGenes breakTranscriptsOnGenes Breaks transcripts on genes
combineTranscripts combineTranscripts Combines transnscipts.
countMappableReadsInInterval countMappableReadsInInterval counts the number of mappable reads in a set of genomic features.
detectTranscripts detectTranscripts detects transcripts de novo using a two-state hidden Markov model (HMM).
evaluateHMMInAnnotations evaluateHMM Evaluates HMM calling.
expressedGenes Function identifies expressed features using the methods introduced in Core, Waterfall, Lis; Science, Dec. 2008.
getCores Returns the number of cores.
getTxDensity getTxDensity Calculates transcript density.
groHMM groHMM: GRO-seq Analysis Pipeline
limitToXkb limitToXkb truncates a set of genomic itnervals at a constant, maximum size.
makeConsensusAnnotations makeConsensusAnnotations Makes a consensus annotation
metaGene Returns a histogram of the number of reads in each section of a moving window centered on a certain feature.
metaGeneMatrix Returns a matrix, with rows representing read counts across a specified gene, or other features of interest.
metaGene_nL Returns a histogram of the number of reads in each section of a moving window of #' variable size across genes.
pausingIndex Returns the pausing index for different genes. TODO: DESCRIBE THE PAUSING INDEX.
polymeraseWave Given GRO-seq data, identifies the location of the polymerase 'wave' in up- or down- regulated genes.
readBed readBed Returns a GenomicRanges object constrcuted from the specified bed file.
RgammaMLE RgammaMLE fits a gamma distribution to a specified data vector using maximum likelihood.
Rnorm Rnorm fits a normal distribution to a specified data vector using maximum likelihood.
Rnorm.exp Rnorm.exp fits a normal+exponential distribution to a specified data vector using maximum likelihood.
runMetaGene Runs metagene analysis for sense and antisense direction.
tlsDeming A 'total least squares' implementation using demming regression.
tlsLoess A 'total least squares'-like hack for LOESS. Works by rotating points 45 degrees, fitting LOESS, and rotating back.
tlsSvd A 'total least squares' implementation using singular value demposition.
windowAnalysis windowAnalysis Returns a vector of integers representing the counts of reads in a moving window.
writeWiggle writeWiggle writes a wiggle track or BigWig file suitable for uploading to the UCSC genome browser.