# GRO-seq Analysis Pipeline

## Documentation for package ‘groHMM’ version 1.14.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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.