# 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 3.45.3

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

A B C D E F G H I M O P R S T W X misc

ChIPpeakAnno-package | 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"'