Convert (a subset of) a raw score matrix to a distance matrix

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. every neuron in scoremat will be used.

See also

Other scoremats: nhclust()