Man pages for jianhong/ChIPpeakAnno
Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data
| 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... |
| addMetadata | Add metadata of the GRanges objects used for... |
| annoGR | Class 'annoGR' |
| annoPeaks | Annotate peaks |
| annotatedPeak | Annotated Peaks |
| annotatePeakInBatch | Obtain the distance to the nearest TSS, miRNA, and/or exon... |
| assignChromosomeRegion | Summarize peak distribution over exon, intron, enhancer,... |
| bdp | obtain the peaks near bi-directional promoters |
| bindist | Class '"bindist"' |
| binOverFeature | Aggregate peaks over bins from the TSS |
| binOverGene | coverage of gene body |
| binOverRegions | coverage of chromosome regions |
| ChIPpeakAnno-deprecated | Deprecated Functions in Package ChIPpeakAnno |
| ChIPpeakAnno-package | Batch annotation of the peaks identified from either ChIP-seq... |
| 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... |
| 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... |
| 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... |
| 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... |
| getEnrichedGO | Obtain enriched gene ontology (GO) terms that near the peaks |
| getEnrichedPATH | Obtain enriched PATH that near the peaks |
| getGeneSeq | Get gene sequence using the biomaRt package |
| getGO | Obtain gene ontology (GO) terms for given genes |
| getUniqueGOidCount | get the count for each unique GO ID |
| getVennCounts | Obtain Venn Counts for Venn Diagram, internal function for... |
| HOT.spots | High Occupancy of Transcription Related Factors regions |
| hyperGtest | hypergeometric test |
| IDRfilter | Filter peaks by IDR (irreproducible discovery rate) |
| 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... |
| 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... |
| peaks2 | An example GRanges object representing a ChIP-seq peak... |
| peaks3 | An example GRanges object representing a ChIP-seq peak... |
| peaksNearBDP | obtain the peaks near bi-directional promoters |
| Peaks.Ste12.Replicate1 | Ste12-binding sites from biological replicate 1 in yeast (see... |
| Peaks.Ste12.Replicate2 | Ste12-binding sites from biological replicate 2 in yeast (see... |
| Peaks.Ste12.Replicate3 | Ste12-binding sites from biological replicate 3 in yeast (see... |
| permPool | 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... |
| summarizePatternInPeaks | Output a summary of the occurrence and enrichment of each... |
| 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... |
| TSS.human.GRCh37 | TSS annotation for human sapiens (GRCh37) obtained from... |
| TSS.human.GRCh38 | TSS annotation for human sapiens (GRCh38) obtained from... |
| TSS.human.NCBI36 | TSS annotation for human sapiens (NCBI36) obtained from... |
| TSS.mouse.GRCm38 | TSS annotation data for Mus musculus (GRCm38.p1) obtained... |
| 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... |
| 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 |
| 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 |
