ChIPpeakAnno-deprecated
                        Deprecated Functions in Package ChIPpeakAnno
ChIPpeakAnno-package    Batch annotation of the peaks identified from
                        either ChIP-seq or ChIP-chip experiments.
EnsDb2GR                EnsDb object to GRanges
ExonPlusUtr.human.GRCh37
                        Gene model with exon, 5' UTR and 3' UTR
                        information for human sapiens (GRCh37) obtained
                        from biomaRt
HOT.spots               High Occupancy of Transcription Related Factors
                        regions
IDRfilter               Filter peaks by IDR (irreproducible discovery
                        rate)
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)
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
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            Class 'annoGR'
annoPeaks               Annotate peaks
annotatePeakInBatch     Obtain the distance to the nearest TSS, miRNA,
                        and/or exon for a list of peaks
annotatedPeak           Annotated Peaks
assignChromosomeRegion
                        Summarize peak distribution over exon, intron,
                        enhancer, proximal promoter, 5 prime UTR and 3
                        prime UTR
bdp                     obtain the peaks near bi-directional promoters
binOverFeature          Aggregate peaks over bins from the TSS
binOverGene             coverage of gene body
binOverRegions          coverage of chromosome regions
bindist-class           Class '"bindist"'
cntOverlaps             count overlaps
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
downstreams             Get downstream coordinates
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
estFragmentLength       estimate the fragment length
estLibSize              estimate the library size
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.
findOverlapsOfPeaks     Find the overlapped peaks among two or more set
                        of peaks.
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
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
oligoFrequency          get the oligonucleotide frequency
oligoSummary            Output a summary of consensus in the peaks
peakPermTest            Permutation Test for two given peak lists
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          Class '"permPool"'
pie1                    Pie Charts
plotBinOverRegions      plot the coverage of regions
preparePool             prepare data for permutation test
reCenterPeaks           re-center the peaks
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.
tileCount               Perform overlap queries between reads and
                        genome by windows
tileGRanges             Slide windows on a given GRanges object
toGRanges               Convert dataset to GRanges
translatePattern        translate pattern from IUPAC Extended Genetic
                        Alphabet to regular expression
wgEncodeTfbsV3          transcription factor binding site clusters (V3)
                        from ENCODE
write2FASTA             Write sequences to a file in fasta format
xget                    Return the value from a Bimap objects
