R/nblast.R
fc_subscoremat.Rd
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"))
query, target | Vectors of FlyCircuit identifiers (Neuron name, gene_name
or integer idid are all acceptable since they will be processed by
|
---|---|
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 |
distance | Logical indicating whether to return distances or scores. |
normalisation | The type of normalisation procedure that should be
carried out, selected from |
big.matrix, ff