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.

estimateFragSize(): estimateFragSize

exampleDNAme geneBodies: Example DNAme data on some active gene bodies

exampleESE: Example EnrichmentSE object

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

motifFootprint(): motifFootprint

plotCorFromCovStats(): plotCorFromCovStats

plotCovStats(): plotCovStats

plotEnrichedHeatmaps(): plotEnrichedHeatmaps: Plots heatmaps of signals around a set of regions

plotSignalTracks(): plotSignalTracks

reduceWithResplit(): Merge regions, re-splitting large merges using local overlap minima

refragment(): refragment

regionCAT(): regionCAT

regionOverlaps(): regionOverlaps

regionUpset(): regionUpset

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