Reference

All functions
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.
advancedArg()	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