Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

Documentation for package ‘ChIPpeakAnno’ version 3.43.1

Help Pages

Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments.

-- A --

addAncestors	Add GO IDs of the ancestors for a given vector of GO ids
addGeneIDs	Add common IDs to annotated peaks such as gene symbol, entrez ID, ensemble gene id and refseq id.
addMetadata	Add metadata of the GRanges objects used for findOverlapsOfPeaks
annoGR	Class 'annoGR'
annoGR-class	Class 'annoGR'
annoGR-method	Class 'annoGR'
annoPeaks	Annotate peaks
annotatedPeak	Annotated Peaks
annotatePeakInBatch	Obtain the distance to the nearest TSS, miRNA, and/or exon for a list of peaks
assignChromosomeRegion	Summarize peak distribution over exon, intron, enhancer, proximal promoter, 5 prime UTR and 3 prime UTR

-- B --

bdp	obtain the peaks near bi-directional promoters
bindist	Class '"bindist"'
bindist-class	Class '"bindist"'
bindist-method	Class '"bindist"'
binOverFeature	Aggregate peaks over bins from the TSS
binOverGene	coverage of gene body
binOverRegions	coverage of chromosome regions

-- C --

ChIPpeakAnno	Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments.
ChIPpeakAnno-deprecated	Deprecated Functions in Package ChIPpeakAnno
cntOverlaps	count overlaps
coerce	Class 'annoGR'
coerce-method	Class 'annoGR'
condenseMatrixByColnames	Condense matrix by colnames
convert2EntrezID	Convert other common IDs to entrez gene ID.
countPatternInSeqs	Output total number of patterns found in the input sequences
cumulativePercentage	Plot the cumulative percentage tag allocation in sample

-- D --

downstreams

Get downstream coordinates

-- E --

egOrgMap	Convert between the name of the organism annotation package ("OrgDb") and the name of the organism.
enrichedGO	Enriched Gene Ontology terms used as example
enrichmentPlot	plot enrichment results
EnsDb2GR	EnsDb object to GRanges
estFragmentLength	estimate the fragment length
estLibSize	estimate the library size
ExonPlusUtr.human.GRCh37	Gene model with exon, 5' UTR and 3' UTR information for human sapiens (GRCh37) obtained from biomaRt

-- F --

featureAlignedDistribution	plot distribution in given ranges
featureAlignedExtendSignal	extract signals in given ranges from bam files
featureAlignedHeatmap	Heatmap representing signals in given ranges
featureAlignedSignal	extract signals in given ranges
findEnhancers	Find possible enhancers depend on DNA interaction data
findMotifsInPromoterSeqs	Find occurence of input motifs in the promoter regions of the input gene list
findOverlappingPeaks	Find the overlapping peaks for two peak ranges.
findOverlappingPeaks-deprecated	Find the overlapping peaks for two peak ranges.
findOverlapsOfPeaks	Find the overlapped peaks among two or more set of peaks.

-- G --

genomicElementDistribution	Genomic Element distribution
genomicElementUpSetR	Genomic Element data for upset plot
getAllPeakSequence	Obtain genomic sequences around the peaks
getAnnotation	Obtain the TSS, exon or miRNA annotation for the specified species
getEnrichedGO	Obtain enriched gene ontology (GO) terms that near the peaks
getEnrichedPATH	Obtain enriched PATH that near the peaks
getGO	Obtain gene ontology (GO) terms for given genes
getVennCounts	Obtain Venn Counts for Venn Diagram, internal function for makeVennDigram

-- H --

HOT.spots

High Occupancy of Transcription Related Factors regions

-- I --

IDRfilter	Filter peaks by IDR (irreproducible discovery rate)
info	Class 'annoGR'
info-method	Class 'annoGR'

-- M --

makeVennDiagram	Make Venn Diagram from a list of peaks
mergePlusMinusPeaks	Merge peaks from plus strand and minus strand
metagenePlot	peak distance to features
myPeakList	An example GRanges object representing a ChIP-seq peak dataset

-- O --

oligoFrequency	get the oligonucleotide frequency
oligoSummary	Output a summary of consensus in the peaks
overlappingPeaks	Find the overlapped peaks among two or more set of peaks.
overlappingPeaks-class	Find the overlapped peaks among two or more set of peaks.

-- P --

peakPermTest	Permutation Test for two given peak lists
Peaks.Ste12.Replicate1	Ste12-binding sites from biological replicate 1 in yeast (see reference)
Peaks.Ste12.Replicate2	Ste12-binding sites from biological replicate 2 in yeast (see reference)
Peaks.Ste12.Replicate3	Ste12-binding sites from biological replicate 3 in yeast (see reference)
peaks1	An example GRanges object representing a ChIP-seq peak dataset
peaks2	An example GRanges object representing a ChIP-seq peak dataset
peaks3	An example GRanges object representing a ChIP-seq peak dataset
peaksNearBDP	obtain the peaks near bi-directional promoters
permPool	Class '"permPool"'
permPool-class	Class '"permPool"'
permPool-method	Class '"permPool"'
pie1	Pie Charts
plotBinOverRegions	plot the coverage of regions
preparePool	prepare data for permutation test

-- R --

reCenterPeaks

re-center the peaks

-- S --

summarizeOverlapsByBins	Perform overlap queries between reads and genomic features by bins
summarizePatternInPeaks	Output a summary of the occurrence and enrichment of each pattern in the sequences.

-- T --

tileCount	Perform overlap queries between reads and genome by windows
tileGRanges	Slide windows on a given GRanges object
toGRanges	Convert dataset to GRanges
toGRanges-method	Convert dataset to GRanges
translatePattern	translate pattern from IUPAC Extended Genetic Alphabet to regular expression
TSS.human.GRCh37	TSS annotation for human sapiens (GRCh37) obtained from biomaRt
TSS.human.GRCh38	TSS annotation for human sapiens (GRCh38) obtained from biomaRt
TSS.human.NCBI36	TSS annotation for human sapiens (NCBI36) obtained from biomaRt
TSS.mouse.GRCm38	TSS annotation data for Mus musculus (GRCm38.p1) obtained from biomaRt
TSS.mouse.NCBIM37	TSS annotation data for mouse (NCBIM37) obtained from biomaRt
TSS.rat.RGSC3.4	TSS annotation data for rat (RGSC3.4) obtained from biomaRt
TSS.rat.Rnor_5.0	TSS annotation data for Rattus norvegicus (Rnor_5.0) obtained from biomaRt
TSS.zebrafish.Zv8	TSS annotation data for zebrafish (Zv8) obtained from biomaRt
TSS.zebrafish.Zv9	TSS annotation for Danio rerio (Zv9) obtained from biomaRt
TxDb2GR	TxDb object to GRanges

-- W --

wgEncodeTfbsV3	transcription factor binding site clusters (V3) from ENCODE
write2FASTA	Write sequences to a file in fasta format

-- X --

xget	Return the value from a Bimap objects

-- misc --

$-method	Class '"bindist"'
$-method	Class '"permPool"'
$<--method	Class '"bindist"'
$<--method	Class '"permPool"'