Package index • epiwraps

All functions

TSSenrichment(): TSSenrichment
addAssayToESE(): addAssayToESE
annotateRegions(): annotateRegions
bam2bw(): bam2bw: create a coverage bigwig file from an alignment bam file.
bamChrChunkApply(): bamChrChunkApply
breakStrings(): breakStrings
callPeaks(): callPeaks
clusterSignalMatrices(): clusterSignalMatrices: clusters the regions of a (set of) signal matrices.
computeDeviationsFaster(): computeDeviationsFaster
estimateFragSize(): estimateFragSize
exampleDNAme geneBodies: Example DNAme data on some active gene bodies
exampleESE: Example EnrichmentSE object
exportNarrowPeaks(): exportNarrowPeaks
formatGenomicDist(): formatGenomicDist
frag2bw(): frag2bw
fragSizesDist(): fragSizesDist
getCovStats(): getCovStats
getEmpiricalFDR(): getEmpiricalFDR
getNormFactors() bwNormFactors(): getNormFactors : estimate normalization factors from genomic signal files
getSignalMatrices(): getSignalMatrices
importBedlike(): importBedlike
inject(): Inject (insert) values at positions in a vector
meltSignals(): meltSignals
mergeSignalMatrices(): mergeSignalMatrices: aggregates two or more signal matrices.
ml2ESE(): Creates an EnrichmentSE from a list of normalizedMatrix objects
motifCoOccurence(): motifCoOccurence
motifFootprint(): motifFootprint
peakCountsFromBAM(): peakCountsFromBAM
peakCountsFromFrags(): peakCountsFromFrags
plotCorFromCovStats(): plotCorFromCovStats
plotCovStats(): plotCovStats
plotEnrichedHeatmaps(): plotEnrichedHeatmaps: Plots heatmaps of signals around a set of regions
plotSignalTracks(): plotSignalTracks
reduceRleLists(): reduceRleLists
reduceWithResplit(): Merge regions, re-splitting large merges using local overlap minima
regionCAT(): regionCAT
regionOverlaps(): regionOverlaps
regionsToUpset(): regionsToUpset
renormalizeBorders() renormalizeSignalMatrices(): renormalizeSignalMatrices
resizeMatrix(): resize a numeric matrix to given dimensions
showTrackInfo(): showTrackInfo
signal2Matrix(): signal2Matrix: reads the signals in/around a set of genomic regions.
signalsAcrossSamples(): signalsAcrossSamples
tabixChrApply(): tabixChrApply
tileRle(): tileRle
views2Matrix(): views2Matrix