Man pages for derfinder
Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

analyzeChrRun the derfinder analysis on a chromosome
annotateRegionsAssign genomic states to regions
calculatePvaluesCalculate p-values and identify regions
calculateStatsCalculate F-statistics at base pair resolution from a loaded...
coerceGRCoerce the coverage to a GRanges object for a given sample
collapseFullCoverageCollapse full coverage information for efficient quantile...
coverageToExonExtract coverage information for exons
createBwExport coverage to BigWig files
createBwSampleCreate a BigWig file with the coverage information for a...
define_clusterDefine a cluster to use.
derfinder-deprecatedDeprecated functions in package 'derfinder'
derfinder-packageAnnotation-agnostic differential expression analysis of...
extendedMapSeqlevelsChange naming style for a set of sequence names
filterDataFilter the positions of interest
findRegionsFind non-zero regions in a Rle
fullCoverageLoad the unfiltered coverage information from a group of BAM...
genomeDataGenome samples processed data
genomeDataRawGenome samples processed data
genomeFstatsF-statistics for the example data
genomeInfoGenome samples information
genomeRegionsCandidate DERs for example data
genomicStateGenomic State for Hsapiens.UCSC.hg19.knownGene
getRegionCoverageExtract coverage information for a set of regions
getTotalMappedCalculate the total number of mapped reads
loadCoverageLoad the coverage information from a group of BAM files
makeGenomicStateObtain the genomic state per region from annotation
makeModelsBuild model matrices for differential expression
mergeResultsMerge results from different chromosomes
preprocessCoverageTransform and split the data
railMatrixIdentify regions data by a coverage filter and get a count...
rawFilesConstruct full paths to a group of raw input files
regionMatrixIdentify regions data by a coverage filter and get a count...
sampleDepthCalculate adjustments for library size
derfinder documentation built on Nov. 17, 2017, 1:43 p.m.