sub_score_mat: Return scores (or distances) for given query and target...

In nat.nblast: NeuroAnatomy Toolbox ('nat') Extension for Assessing Neuron Similarity and Clustering

Return scores (or distances) for given query and target neurons

Description

Scores can either be returned as raw numbers, normalised such that a self-hit has score 1, or as the average of the normalised scores in both the forwards & reverse directions (i.e. |query->target| + |target->query| / 2). Distances are returned as either 1 - normscore in the forwards direction, or as 1 - normscorebar, where normscorebar is normscore averaged across both directions.

Usage

sub_score_mat(
  query,
  target,
  scoremat = NULL,
  distance = FALSE,
  normalisation = c("raw", "normalised", "mean")
)

Arguments

query, target	character vectors of neuron identifiers.
scoremat	a matrix, ff matrix, bigmatrix or a character vector specifying the name of an ff matrix containing the all by all score matrix.
distance	logical indicating whether to return distances or scores.
normalisation	the type of normalisation procedure that should be carried out, selected from 'raw', 'normalised' or 'mean' (i.e. the average of normalised scores in both directions). If distance=TRUE then this cannot be raw.

See Also

sub_dist_mat

nat.nblast documentation built on July 9, 2023, 6:12 p.m.