FunChIP

FunChIP analyzes ChIP-seq peak shapes in R/Bioconductor by preprocessing and smoothing peaks, approximating peak profiles with cubic B-splines, and clustering peaks by minimized functional distance to investigate protein–DNA interactions and chromatin modifications.

Key Features:

• Preprocessing and smoothing: Initial smoothing of ChIP-seq peaks to prepare profiles for shape analysis.
• Shape approximation with cubic B-splines: Approximates peak profiles using cubic B-splines to capture functional representations of peak shape.
• Functional distance minimization (k-mean alignment and clustering): Minimizes functional distance between peaks using k-mean alignment and clustering to classify peaks by shape.
• Visualization functions: Provides visualization routines to inspect and present clustered peak shapes.

Scientific Applications:

• Association of peak shapes with regulatory activity: Associates clusters of peaks with distinct genomic locations and transcriptional regulatory activities.
• Myc in 3T9 murine fibroblasts: Analysis of Myc ChIP-seq in 3T9 murine fibroblasts showed that peak shape variations correlate with diverse functional outcomes.

Methodology:

Preprocessing (smoothing of ChIP-seq peaks); shape approximation with cubic B-splines; and k-mean alignment and clustering minimizing functional distance.