sub_dist_mat: Convert (a subset of) a raw score matrix to a distance matrix
Description
This function can convert a raw score matrix returned by nblast
into a square distance matrix or dist object. It can be used with
file-backed matrices as well as regular R matrices resident in memory.
Usage
sub_dist_mat(neuron_names, scoremat = NULL, form = c("matrix", "dist"), maxneurons = NA)
Arguments
neuron_names
character vector of neuron identifiers.
scoremat
score matrix to use (see sub_score_mat for details of
default).
form
the type of object to return.
maxneurons
set this to a sensible value to avoid loading huge (order
N^2) distances directly into memory.
Value
return An object of class matrix or dist (as determined by the form
argument), corresponding to a subset of the distance matrix
Details
Note that if neuron_names is missing then the rownames of
scoremat will be used i.e. all neuron in scoremat will be used.