# Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges.

## Documentation for package ‘ChIPpeakAnno’ version 3.2.2

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

## Help Pages

ChIPpeakAnno-package | Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments.
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.
annotatedPeak | Annotated Peaks
annotatePeakInBatch | obtain the distance to the nearest TSS, miRNA, exon et al for a list of peak intervals
assignChromosomeRegion | Summarizing peak distribution over exon, intron, enhancer, proximal promoter, 5 prime UTR and 3 prime UTR
BED2RangedData | convert BED format to RangedData
binOverFeature | peak aggregation over bins from TSS
ChIPpeakAnno | Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments.
ChIPpeakAnno-deprecated | Deprecated Functions in Package ChIPpeakAnno
condenseMatrixByColnames | condense matrix by colnames
convert2EntrezID | Convert other common IDs such as ensemble gene id, gene symbol, refseq id to entrez gene ID.
countPatternInSeqs | Output total number of patterns found in the input sequences
egOrgMap | map organism annotation dataset to specie name or revese.
enrichedGO | Enriched Gene Ontology terms used as example
ExonPlusUtr.human.GRCh37 | Gene model with exon, 5' UTR and 3' UTR information for human sapiens (GRCh37) obtained from biomaRt
findOverlappingPeaks | Find the overlapping peaks for two peak ranges.
findOverlappingPeaks-deprecated | Find the overlapping peaks for two peak ranges.
findOverlapsOfPeaks | Find the overlapping peaks for two or more peak ranges.
findVennCounts | Obtain Venn Counts for Venn Diagram, internal function for makeVennDigram
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
getVennCounts | Obtain Venn Counts for Venn Diagram, internal function for makeVennDigram
GFF2RangedData | convert GFF format to RangedData
makeVennDiagram | Make Venn Diagram from two peak ranges
myPeakList | ChIP-seq peak dataset
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)
peaksNearBDP | obtain the peaks near bi-directional promoters
summarizePatternInPeaks | Output a summary of the occurrence of each pattern in the sequences.
toGRanges | 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
write2FASTA | write sequences to a file in fasta format