# An R package to detect chromatin state switches from epigenomic data

## Documentation for package ‘chromswitch’ version 1.4.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

chromswitch-package | chromswitch: An R package for detecting chromatin state switches
binarizePeaks | binarizePeaks
callBinary | callBinary
callSummary | callSummary
chromswitch | chromswitch: An R package for detecting chromatin state switches
classEntropy | classEntropy
cluster | cluster
clusterEntropy | clusterEntropy
completeness | completeness
conditionalClassEntropy | classEntropyGivenClusters
conditionalClusterEntropy | clusterEntropyGivenClasses
coordToGRanges | coordToGRanges
filterPeaks | filterPeaks
GRangesToCoord | GRangesToCoord
H3K4me3 | H3K4me3 peak calls in a short region for six adult tissues
homogeneity | homogeneity
LocalPeaks | LocalPeaks
LocalPeaks-class | LocalPeaks
makeBrowserCoord | makeBrowserCoord
NMI | NMI
normalizePeaks | normalizePeaks
peaks | LocalPeaks
peaks-method | LocalPeaks
pReciprocalOverlap | pReciprocalOverlap
purity | purity
readNarrowPeak | readNarrowPeak
reducePeaks | reducePeaks
region | LocalPeaks
region-method | LocalPeaks
retrievePeaks | retrievePeaks
samples | LocalPeaks
samples-method | LocalPeaks
summarizePeaks | summarizePeaks
vMeasure | vMeasure
winsorNorm | winsorNorm
\S4method{peaks}{LocalPeaks} | LocalPeaks
\S4method{region}{LocalPeaks} | LocalPeaks
\S4method{samples}{LocalPeaks} | LocalPeaks