# Nucleosome positioning package for R

## 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