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

addAncestorsAdd GO IDs of the ancestors for a given vector of GO ids
addGeneIDsAdd common IDs to annotated peaks such as gene symbol, entrez...
addMetadataAdd metadata of the GRanges objects used for...
annoGRClass 'annoGR'
annoPeaksAnnotate peaks
annotatedPeakAnnotated Peaks
annotatePeakInBatchObtain the distance to the nearest TSS, miRNA, and/or exon...
assignChromosomeRegionSummarize peak distribution over exon, intron, enhancer,...
bdpobtain the peaks near bi-directional promoters
BED2RangedDataConvert BED format to RangedData
bindistClass '"bindist"'
binOverFeatureAggregate peaks over bins from the TSS
ChIPpeakAnno-deprecatedDeprecated Functions in Package ChIPpeakAnno
ChIPpeakAnno-packageBatch annotation of the peaks identified from either ChIP-seq...
condenseMatrixByColnamesCondense matrix by colnames
convert2EntrezIDConvert other common IDs to entrez gene ID.
countPatternInSeqsOutput total number of patterns found in the input sequences
cumulativePercentagePlot the cumulative percentage tag allocation in sample
egOrgMapConvert between the name of the organism annotation package...
enrichedGOEnriched Gene Ontology terms used as example
estFragmentLengthestimate the fragment length
estLibSizeestimate the library size
ExonPlusUtr.human.GRCh37Gene model with exon, 5' UTR and 3' UTR information for human...
featureAlignedDistributionplot distribution in given ranges
featureAlignedExtentSignalextract signals in given ranges from bam files
featureAlignedHeatmapHeatmap representing signals in given ranges
featureAlignedSignalextract signals in given ranges
findEnhancersFind possible enhancers depend on DNA interaction data
findOverlappingPeaksFind the overlapping peaks for two peak ranges.
findOverlapsOfPeaksFind the overlapped peaks among two or more set of peaks.
findVennCountsObtain Venn Counts for Venn Diagram, internal function for...
getAllPeakSequenceObtain genomic sequences around the peaks
getAnnotationObtain the TSS, exon or miRNA annotation for the specified...
getEnrichedGOObtain enriched gene ontology (GO) terms that near the peaks
getEnrichedPATHObtain enriched PATH that near the peaks
getGeneSeqGet gene sequence using the biomaRt package
getUniqueGOidCountget the count for each unique GO ID
getVennCountsObtain Venn Counts for Venn Diagram, internal function for...
GFF2RangedDataConvert GFF format to RangedData
HOT.spotsHigh Occupancy of Transcription Related Factors regions
hyperGtesthypergeometric test
IDRfilterFilter peaks by IDR (irreproducible discovery rate)
makeVennDiagramMake Venn Diagram from a list of peaks
mergePlusMinusPeaksMerge peaks from plus strand and minus strand
myPeakListAn example GRanges object representing a ChIP-seq peak...
oligoFrequencyget the oligonucleotide frequency
oligoSummaryOutput a summary of consensus in the peaks
peakPermTestPermutation Test for two given peak lists
peaksNearBDPobtain the peaks near bi-directional promoters
Peaks.Ste12.Replicate1Ste12-binding sites from biological replicate 1 in yeast (see...
Peaks.Ste12.Replicate2Ste12-binding sites from biological replicate 2 in yeast (see...
Peaks.Ste12.Replicate3Ste12-binding sites from biological replicate 3 in yeast (see...
permPoolClass '"permPool"'
pie1Pie Charts
preparePoolprepare data for permutation test
reCenterPeaksre-center the peaks
summarizeOverlapsByBinsPerform overlap queries between reads and genomic features by...
summarizePatternInPeaksOutput a summary of the occurrence of each pattern in the...
tileCountPerform overlap queries between reads and genome by windows
tileGRangesSlide windows on a given GRanges object
toGRangesConvert dataset to GRanges
translatePatterntranslate pattern from IUPAC Extended Genetic Alphabet to...
TSS.human.GRCh37TSS annotation for human sapiens (GRCh37) obtained from...
TSS.human.GRCh38TSS annotation for human sapiens (GRCh38) obtained from...
TSS.human.NCBI36TSS annotation for human sapiens (NCBI36) obtained from...
TSS.mouse.GRCm38TSS annotation data for Mus musculus (GRCm38.p1) obtained...
TSS.mouse.NCBIM37TSS annotation data for mouse (NCBIM37) obtained from biomaRt
TSS.rat.RGSC3.4TSS annotation data for rat (RGSC3.4) obtained from biomaRt
TSS.rat.Rnor_5.0TSS annotation data for Rattus norvegicus (Rnor_5.0) obtained...
TSS.zebrafish.Zv8TSS annotation data for zebrafish (Zv8) obtained from biomaRt
TSS.zebrafish.Zv9TSS annotation for Danio rerio (Zv9) obtained from biomaRt
wgEncodeTfbsV3transcription factor binding site clusters (V3) from ENCODE
write2FASTAWrite sequences to a file in fasta format
xgetReturn the value from a Bimap objects
ChIPpeakAnno documentation built on May 31, 2017, 11:32 a.m.