calc_score_matrix

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

Extends package 'nat' (NeuroAnatomy Toolbox) by providing a
collection of NBLAST-related functions for neuronal morphology comparison (Costa et al. (2016) <doi: 10.1016/j.neuron.2016.06.012>).

Gregory Jefferis

nat.nblast

NeuroAnatomy Toolbox ('nat') Extension for Assessing Neuron
Similarity and Clustering

James Manton

calc_score_matrix function

<dl><dt>matchmat</dt>
<dd>a probability matrix given by considering 'matching' neurons.</dd>
<dt>randmat</dt>
<dd>a probability matrix given by considering 'non-matching' or
'random' neurons.</dd>
<dt>logbase</dt>
<dd>the base to which the logarithm should be taken to produce the
final scores.</dd>
<dt>epsilon</dt>
<dd>a pseudocount to prevent division by zero when constructing
the log odds ratio in the probability matrix.</dd></dl>

Arguments

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

<dl>

<dt>matchmat</dt>
<dd>a probability matrix given by considering 'matching' neurons.</dd>


<dt>randmat</dt>
<dd>a probability matrix given by considering 'non-matching' or
'random' neurons.</dd>


<dt>logbase</dt>
<dd>the base to which the logarithm should be taken to produce the
final scores.</dd>


<dt>epsilon</dt>
<dd>a pseudocount to prevent division by zero when constructing
the log odds ratio in the probability matrix.</dd>

</dl>

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

Description

Usage

Value

Arguments