Call wide peaks for sequencing data


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Documentation for package ‘NADfinder’ version 1.0.1

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NADfinder-package Call peaks for nucleolar-associated domains (NADs) sequencing data
backgroundCorrection Correct ratios for background
butterFilter Low pass filter on ratios by butterworth filter
callPeaks call peaks for ratios of repeats
countByOverlaps Count overlapping genomic ranges
cumulativePercentage Plot the cumulative percentage tag allocation in sample
exportSignals output signals to file
getCorrelations get correlations for replicates
groupZscores Calculate z-scores for each peak
log2ratio calculate the log2 transformed ratios
log2se calculate the log2 transformed ratios for SummarizedExperiment class
NADfinder Call peaks for nucleolar-associated domains (NADs) sequencing data
peakdet Detect peak positions
plotSig plot signals with ideograms
single.count counts data for single experiment of chromosome 18
smoothRatiosByChromosome smooth the ratios by chromosome
tileCount Perform overlap queries between reads and genome by windows
trimPeaks Trim peaks
triplicates.counts counts data for triplicates of chromosome 18
zscoreOverBck Z-scores over the background