Convenience for creating an SRFilter object appropriate for ChIP-seq data. Typically, the result is passed to readAligned when loading reads.
● Data Source:
BioConductor
● Keywords:
● Alias: chipseqFilter
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A function that plots one or two coverage vectors over a relatively small interval in the genome.
● Data Source:
BioConductor
● Keywords: hplot
● Alias: coverageplot
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diffPeakSummary
(Package: chipseq) :
A function to identify and produce summary statistics for differentially expressed peaks.
Given two sets of peaks, this function combines them and summarizes the individual coverage vectors under the combined peak set.
● Data Source:
BioConductor
● Keywords:
● Alias: diffPeakSummary, diffPeakSummary,RleViewsList,RleViewsList-method
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estimate.mean.fraglen implements three methods for estimating mean fragment length. The other functions are related helper functions implementing various methods, but may be useful by themselves for diagnostic purposes. Many of these operations are potentially slow.
● Data Source:
BioConductor
● Keywords: univar
● Alias: estimate.mean.fraglen, estimate.mean.fraglen,AlignedRead-method, estimate.mean.fraglen,GRanges-method
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Plots the distribution of island depths using points for the observed islands and a line for the Poisson estimate of the noise. Useful for choosing a depth corresponding to a desired FDR.
● Data Source:
BioConductor
● Keywords:
● Alias: islandDepthPlot
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1 images
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Subsamples data from multiple lanes on a per-chromosome basis.
● Data Source:
BioConductor
● Keywords: manip, utilities
● Alias: laneSubsample
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Calculates a peak cutoff value given an FDR, assuming a Poisson noise distribution estimated from the frequency of singleton and doubleton islands.
● Data Source:
BioConductor
● Keywords:
● Alias: peakCutoff
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Summarizes a set of peaks into a RangedData object with columns of statistics like the peak maxima and integrals (sums).
● Data Source:
BioConductor
● Keywords: methods
● Alias: peakSummary, peakSummary,RleViews-method, peakSummary,RleViewsList-method, peakSummary-methods
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THIS FUNCTION IS DEFUNCT!
● Data Source:
BioConductor
● Keywords: univar
● Alias: subsetSummary
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providing 
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