Nucleosome positioning package for R


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Documentation for package ‘nucleR’ version 2.36.0

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nucleR-package Nucleosome positioning package for R
.fftRegion FFT Region
.getThreshold Threshold getter
.loadFiles File loader Higher order function to import BAM or Bowtie files. Deals with wether type is 'single' or 'paired' and with the number of input files
.loadPairedBam Load a paired-end-end BAM
.loadSingleBam Load a single-end BAM
.mid Find midpoints
.processStrand Process a given strand from a BAM file to read
.unlist_as_integer Unlist an IRanges object into a vector
.vectorizedAll Vectorized version of 'all'
.xlapply mclapply warapper
controlCorrection Correct experimental profiles with control sample
controlCorrection-method Correct experimental profiles with control sample
coverage.rpm Coverage calculation and normalization to reads per million (rpm)
coverage.rpm-method Coverage calculation and normalization to reads per million (rpm)
export.bed Export ranges in BED format
export.bed-method Export ranges in BED format
export.wig Export values in WIG format
filterFFT Clean noise and smoothing for genomic data using Fourier-analysis
filterFFT-method Clean noise and smoothing for genomic data using Fourier-analysis
fragmentLenDetect Fragments length detection from single-end sequencing samples
fragmentLenDetect-method Fragments length detection from single-end sequencing samples
mergeCalls Automatic merging of overlapped nucleosome calls
mergeCalls-method Automatic merging of overlapped nucleosome calls
nucleosome_htseq Example reads from high-troughtput sequencing nucleosome positioning experiment
nucleosome_tiling Example intensities from Tiling Microarray nucleosome positioning experiment
nucleR Nucleosome positioning package for R
pcKeepCompDetect Auto detection of a fitted 'pcKeepComp' param for filterFFT function
peakDetection Detect peaks (local maximum) from values series
peakDetection-method Detect peaks (local maximum) from values series
peakScoring Peak scoring function
peakScoring-method Peak scoring function
plotPeaks Nucleosome calling plot function
plotPeaks-method Nucleosome calling plot function
processReads Process reads from High-Troughtput Sequencing experiments
processReads-method Process reads from High-Troughtput Sequencing experiments
processTilingArray Obtain and clean nucleosome positioning data from tiling array
readBAM Import reads from a list of BAM files.
readBowtie Import reads from a vector of Bowtie files
syntheticNucMap Generates a synthetic nucleosome map