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. |