bin_curve: Bins a single scan curve into peaks automatically

In cape: Combined Analysis of Pleiotropy and Epistasis for Diversity Outbred Mice

Bins a single scan curve into peaks automatically

Description

This is an internal function used to select markers for the pair scan based on single scan results. The algorithm first finds the difference between all runs of all positive and all negative values. It smooths the curve and identifies peaks exceeding the threshold defined by amp_min.

Usage

bin_curve(the_curve, plot_peaks = FALSE, window_size = NULL, amp_min = NULL)

Arguments

the_curve	vector representing the curve to be binned into peaks
plot_peaks	default = FALSE
window_size	A numeric value setting how many markers should be included in each window. If NULL, the window size is set to the maximum number of consecutive rises or falls in the curve
amp_min	A numeric value indicating the minimum magnitude of a peak. All peaks below this magnitude will be removed. If NULL amp_min is set to the sd of the curve/2.

Value

This function returns a list with the following elements: bins: a vector the same length as the input curve identifying which peak each position was assigned to. smoothed_curve: A vector defining the smoothed curve window_size: The input window_size or the calculated window_size if window_size was NULL amp_min: the input amp_min or calculated amp_min if amp_min was NULL

cape documentation built on May 29, 2024, 5:11 a.m.