analyzeChr              Run the derfinder analysis on a chromosome
annotateRegions         Assign genomic states to regions
calculatePvalues        Calculate p-values and identify regions
calculateStats          Calculate F-statistics at base pair resolution
                        from a loaded BAM files
coerceGR                Coerce the coverage to a GRanges object for a
                        given sample
collapseFullCoverage    Collapse full coverage information for
                        efficient quantile computations
coverageToExon          Extract coverage information for exons
createBw                Export coverage to BigWig files
createBwSample          Create a BigWig file with the coverage
                        information for a given sample
define_cluster          Define a cluster to use.
derfinder-deprecated    Deprecated functions in package 'derfinder'
extendedMapSeqlevels    Change naming style for a set of sequence names
filterData              Filter the positions of interest
findRegions             Find non-zero regions in a Rle
fullCoverage            Load the unfiltered coverage information from a
                        group of BAM files and a list of chromosomes
genomeData              Genome samples processed data
genomeDataRaw           Genome samples processed data
genomeFstats            F-statistics for the example data
genomeInfo              Genome samples information
genomeRegions           Candidate DERs for example data
genomicState            Genomic State for Hsapiens.UCSC.hg19.knownGene
getRegionCoverage       Extract coverage information for a set of
                        regions
getTotalMapped          Calculate the total number of mapped reads
loadCoverage            Load the coverage information from a group of
                        BAM files
makeGenomicState        Obtain the genomic state per region from
                        annotation
makeModels              Build model matrices for differential
                        expression
mergeResults            Merge results from different chromosomes
preprocessCoverage      Transform and split the data
railMatrix              Identify regions data by a coverage filter and
                        get a count matrix from BigWig files
rawFiles                Construct full paths to a group of raw input
                        files
regionMatrix            Identify regions data by a coverage filter and
                        get a count matrix
sampleDepth             Calculate adjustments for library size
