Return (normalised) nblast similarity scores for FlyCircuit neurons

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"))

Arguments

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

Value

Matrix of scores, columns are query neurons, rows, target.

Details

See the package vignette for an examlple of how to download a precomputed score matrix.

See also

hclustfc