get_scores: get_scores

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

get_scores

Description

This function takes a distance matrix, a presence-absence matrix, a choice of how to determine close pairs, and a list of relevant parameters for that choice, and returns the close pair scores.

Usage

get_scores(
  pa_matrix,
  distance_matrix,
  closepair_method,
  closepair_params,
  blocksize,
  verbose
)

Arguments

pa_matrix	A presence-absence matrix for the trait in question (i.e. gene, allele, phenotype, etc.). Rows are trait, columns are sample. Rownames should be trait names, colnames should be sample names.
distance_matrix	A distance matrix. Rownames and colnames should be sample names and should be in the same order as the columns in pa_matrix.
closepair_method	Either 'distance', 'fraction', 'fixednumber', or 'auto'.
closepair_params	A list. For 'distance', the distance cutoff and show_hist. For 'fraction', the fraction and show_hist. For 'fixednumber', the number of close pairs, a random seed, and show_hist. For 'auto', the which_valley, nbins, maxvalleyheight, and show_hist. verbose is inherited from the main function call.
blocksize	The number of traits to consider at once in the computation. Changing this number may help speed up the computation. Try 100 first.
verbose	TRUE for progress reports. FALSE for no reports.

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