Function reference • derfinder

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

Reference

All functions