epiSeeker: an R package for Annotation, Comparison and Visualization of multi-omics epigenetic data

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Documentation for package ‘epiSeeker’ version 0.99.14

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

Help Pages

.	.
.epiSeekerEnv	Env function for epiSeeker
annotateSeq	annotateSeq
arrange.GRanges	Arrange GRanges object
as.data.frame.csAnno	as.data.frame.csAnno
as.GRanges	as.GRanges
bin_vector	bin vector function
bmData	Constructor for bmData objects
bmData-class	bmData Class
bmData-methods	getBmMatrix methods generics
BSseq-methods	getBmMatrix methods generics
check_bin	check bin parameter method
check_extension	check upstream and downstream extension
check_windows	check windows function
combine_csAnno	combine_csAnno
create_regex_patterns_negative	create regex patterns in negative strand
create_regex_patterns_positive	create regex patterns in positive strand
csAnno-class	Class "csAnno" This class represents the output of epiSeeker Annotation
demo_bmdata	demo base modification data
demo_peak	demo peak file
downloadGEObedFiles	downloadGEObedFiles
downloadGSMbedFiles	downloadGSMbedFiles
dropAnno	dropAnno
enrichAnnoOverlap	enrichAnnoOverlap
enrichPeakOverlap	enrichPeakOverlap
epiSeekerCache	Name of the epiSeeker cache environment (internal static variable)
extend_gr	Extend regions functions
filter.GRanges	Extend filter to Peak (GRanges class object)
getAnnoStat	getAnnoStat
getBioRegion	Prepare a bioregion of selected feature
getBmMatrix	getBmMatrix methods generics
getBmMatrix,	getBmMatrix methods generics
getBmMatrix-method	getBmMatrix methods generics
getBmMatrix.bmData	get the information of base modification
getBmMatrix.BSseq	Get the information of base modification
getGeneAnno	getGeneAnno
getGenomicAnnotation	getGenomicAnnotation
getGEOgenomeVersion	getGEOgenomeVersion
getGEOInfo	getGEOInfo
getGEOspecies	getGEOspecies
getMotifMatrix	Get the information of motif in a range
getNearestFeatureIndicesAndDistances	getNearestFeatureIndicesAndDistances
getPromoters	Get promoter region in GRanges format
getSampleFiles	getSampleFiles
getTagMatrix	getTagMatrix
getTagMatrix.internal	getTagMatrix internal function
getTagMatrix_body	getTagMatrix function for region of body
getTagMatrix_body_internal	get tagmatrix internal function
getTagMatrix_site	getTagMatrix function for region of site
grange2mt	change a list grange object to matrix
gsminfo	Information Datasets
loadTxDb	load defaulst txdb
makeBmDataFromData	makeBmDataFromData method generics
makeBmDataFromData-method	makeBmDataFromData method generics
makeBmDataFromData.internal	makeBmDataFromData.internal
makeBmDataFromFiles	make bmData from files
mutate.GRanges	Extend mutate to Peak (GRanges class object)
overlap	overlap
parse_peak	parse peak str
peakAnno	Example data of peak annotation
peakAnnoList	Example data of a list of peak annotation
plotAnnoBar	plotAnnoBar method generics
plotAnnoBar-method	Class "csAnno" This class represents the output of epiSeeker Annotation
plotAnnoBar-method	plotAnnoBar method generics
plotAnnoBar.data.frame	plotAnnoBar.data.frame
plotAnnoPie	plotAnnoPie method generics
plotAnnoPie-method	Class "csAnno" This class represents the output of epiSeeker Annotation
plotAnnoPie-method	plotAnnoPie method generics
plotAnnoPie.csAnno	plotAnnoPie
plotBmProf	plotBmProf
plotCov	plotCov
plotDistToTSS	plotDistToTSS method generics
plotDistToTSS-method	Class "csAnno" This class represents the output of epiSeeker Annotation
plotDistToTSS-method	plotDistToTSS method generics
plotDistToTSS.data.frame	plotDistToTSS.data.frame
plotGeneTrack	Plot gene track
plotMotifProf	Plot the profile of motif of specific peak
plotPeakHeatmap	plotPeakHeatmap function
plotPeakHeatmap_sub	Plot peak heatmap sub function
plotPeakHeatmap_sub.internal	internal function of plotPeakHeatmap
plotPeakProf	plot peak profile
pwm_obj	motif reference for Homo sapiens
readPeakFile	readPeakFile
rename.GRanges	Rename columns of a GRanges object
seq2gene	seq2gene
seq2gene_result	Result of seq2gene
show	show method
show-method	Class "csAnno" This class represents the output of epiSeeker Annotation
show-method	show method
shuffle	shuffle
subset-method	Class "csAnno" This class represents the output of epiSeeker Annotation
tagMatrix	Example data of tagMatrix
ucsc_release	Information Datasets
upsetplot	upsetplot method
upsetplot-method	Class "csAnno" This class represents the output of epiSeeker Annotation
vennpie	vennpie method generics
vennpie-method	Class "csAnno" This class represents the output of epiSeeker Annotation
vennplot	vennplot
vennplot.peakfile	vennplot.peakfile