summit_peak-method: Finding the summits of the peaks of the GRanges object

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

Description

It identifies the summit of the peak and stores it in a new metadata column.

Usage

## S4 method for signature 'GRanges'
summit_peak(object, summit = NULL, rescale = FALSE)

Arguments

object	GRanges object of length N. If summit is not provided, object must contain the metadata column spline.
summit	vector of length N. It contains the x coordinate of the summit of the peaks, i.e. the distance of the summit from the starting position of the spline approximation of peak (distance from start_spline). If summit is NULL the summit of each peak is identified as the maximum point of the spline.
rescale	logical. If TRUE the distance among scaled peaks is computed. For the definition of scaled peaks see smooth_peak.

Value

the GRanges object with the new metadata column summit_spline. In case of rescale = TRUE an extra metadata column summit_spline_rescaled is added, containing the summit of the scaled peak.

Author(s)

Alice Parodi, Marco J. Morelli, Laura M. Sangalli, Piercesare Secchi, Simone Vantini

Examples

# load the data
data(peaks)

# Computing the summits of the peaks from
# the spline-smoothed approximation.

peaks.spline.summit <- summit_peak(peaks.data.smooth)

FunChIP documentation built on Nov. 8, 2020, 4:50 p.m.