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 3.30.1

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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)
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 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"'
_PACKAGE Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments.