calc_score_matrix {nat.nblast}

Calculate scoring matrix from probability matrices for matching and non-matching sets of neurons

Description

Calculate scoring matrix from probability matrices for matching and non-matching sets of neurons

Usage

calc_score_matrix(matchmat, randmat, logbase = 2, epsilon = 1e-06)

Arguments

matchmat

a probability matrix given by considering 'matching' neurons.

randmat

a probability matrix given by considering 'non-matching' or 'random' neurons.

logbase

the base to which the logarithm should be taken to produce the final scores.

epsilon

a pseudocount to prevent division by zero when constructing the log odds ratio in the probability matrix.

Value

A matrix with with class=c("scoringmatrix", "table"), with columns as specified by dotprodbreaks and rows as specified by distbreaks, containing scores for neuron segments with the given distance and dot product.