Clustering and Alignment of ChIP-Seq peaks based on their shapes

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Documentation for package ‘FunChIP’ version 1.16.0

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FunChIP-package Clustering and Alignment of ChIP-Seq peaks based on their shapes
bending_index The elbow rule to define the proper number of clusters.
choose_k Choice of the final classification of peaks
choose_k-method Choice of the final classification of peaks
cluster_peak Clustering the peaks with the k-mean alignment algorithm
cluster_peak-method Clustering the peaks with the k-mean alignment algorithm
compute_fragments_length Computing the length of the fragments in the .bam file.
distance_peak Computing distance matrices among spline-smoothed peaks and among their derivatives.
FunChIP Clustering and Alignment of ChIP-Seq peaks based on their shapes
GR Peaks of a ChIP-seq experiment
GR100 Peaks of a ChIP-seq experiment
peaks Coverage of a ChIP-Seq experiment
peaks.data Coverage of a ChIP-Seq experiment
peaks.data.classified Coverage of a ChIP-Seq experiment
peaks.data.classified.scaled Coverage of a ChIP-Seq experiment
peaks.data.cluster Coverage of a ChIP-Seq experiment
peaks.data.cluster.scaled Coverage of a ChIP-Seq experiment
peaks.data.smooth Coverage of a ChIP-Seq experiment
peaks.data.smooth.scaled Coverage of a ChIP-Seq experiment
peaks.data.summit Coverage of a ChIP-Seq experiment
peaks.data.summit.scaled Coverage of a ChIP-Seq experiment
pileup_peak Computing read counts on a GRanges object.
pileup_peak-method Computing read counts on a GRanges object.
plot_peak Plotting the peaks.
plot_peak-method Plotting the peaks.
silhouette_plot Return the silhouette index for clustered peaks
smooth_peak Spline smoothing of the peak
smooth_peak-method Spline smoothing of the peak
summit_peak Finding the summits of the peaks of the GRanges object
summit_peak-method Finding the summits of the peaks of the GRanges object