fc_nblast | R Documentation |
Precomputed scores are stored in bigmatrix form on disk. The bigmatrix object
is created in the global environment once per session and then reused. When
normalisation='normalised'
, scores are in the interval [-1, 1] or,
more exactly, range(scorematrix), as the raw scores are divided by the
self-match score. Higher is always better. When normalisation='mean'
,
the returned scores are the mean of the normalised forward and reverse scores
(as used for clustering in hclustfc
) but are similarity scores
(not distances).
fc_nblast( query, target, scoremat = getOption("flycircuit.scoremat"), normalisation = c("raw", "normalised", "mean") )
query |
Vectors of FlyCircuit identifiers (Neuron name, gene_name
or integer idid are all acceptable since they will be processed by
|
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 |
normalisation |
the type of normalisation procedure that should be
carried out, selected from |
See the package vignette for an examlple of how to download a precomputed score matrix.
Matrix of scores, columns are query neurons, rows, target.
hclustfc
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