Package 'ChIPpeakAnno' - Bioconductor

34 summarizePatternInPeaksAuthor(s)Lihua Julie ZhuReferencesZhu L.J. et al. (2010) ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chipdata. BMC Bioinformatics 2010, 11:237doi:10.1186/1471-2105-11-237See AlsoannotatePeakInBatch, findOverlappingPeaks, makeVennDiagramExamplesif (interactive()){data(myPeakList)data(TSS.human.NCBI36)annotatedBDP = peaksNearBDP(myPeakList[1:6,], AnnotationData=TSS.human.NCBI36,MaxDistance=5000,PeakLocForDistance = "middle",FeatureLocForDistance = "TSS")c(annotatedBDP$percentPeaksWithBDP, annotatedBDP$n.peaks, annotatedBDP$n.peaksWithBDP)}summarizePatternInPeaksOutput a summary of the occurrence of each pattern in the sequences.DescriptionUsageOutput a summary of the occurrence of each pattern in the sequences.summarizePatternInPeaks(patternFilePath, format = "fasta",skip=0L, BSgenomeName, peaks, outfile, appenArgumentspatternFilePathA character vector containing the path to the file to read the patterns from.format Either "fasta" (the default) or "fastq"skipSingle non-negative integer. The number of records of the pattern file to skipbefore beginning to read in records.BSgenomeName BSgenome object. Please refer to available.genomes in BSgenome package fordetailspeaksRangedData containing the peaksoutfile A character vector containing the path to the file to write the summary output.append TRUE or FALSE, default FALSE