Nucleosome positioning package for R

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Documentation for package ‘nucleR’ version 2.41.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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