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

Source: R/nblast.R

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.

fc_subscoremat(query, target,
  scoremat = getOption("flycircuit.scoremat"), distance = FALSE,
  normalisation = c("raw", "normalised", "mean"))

Arguments

query, target

Vectors of FlyCircuit identifiers (Neuron name, gene_name or integer idid are all acceptable since they will be processed by fc_gene_name).
scoremat

A matrix, ff matrix, bigmatrix or a character vector specifiying the name of an ff matrix containing the all by all score matrix. Defaults to value of options(flycircuit.scoremat).
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

big.matrix, ff