get_closepairs_distance: get_closepairs_distance

In weissmanlab/decotur: DeCoTUR (Detecting Coevolving Traits Using Relatives)

get_closepairs_distance

Description

This function takes a distance matrix and finds all pairs of samples that are within a specified distance cutoff. The pairs are returned as an nx2 matrix, where n is the number of close pairs, and the elements of the matrix are the indices of the samples in that close pair in the distance matrix.

Usage

get_closepairs_distance(distance_matrix, distance_cutoff, show_hist, verbose)

Arguments

distance_matrix	A distance matrix
distance_cutoff	An inclusive distance cutoff.
show_hist	Boolean indicator for whether or not to plot a histogram of the distances and cutoff. Uses ggplot defaults for bins.
verbose	TRUE to print distance cutoff, FALSE otherwise

Examples

get_closepairs_distance(distance_matrix, 0.0005)

weissmanlab/decotur documentation built on Sept. 4, 2024, 6:49 a.m.