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

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Documentation for package ‘ChIPpeakAnno’ version 2.14.1

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