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

## Documentation for package ‘FunChIP’ version 1.12.0

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

## Help Pages

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