neuronBag: Create a neuronBag

In jayaraman-lab/neuprintrExtra: Extra functions to analyze neuprint EM datasets

Description

Builds a neuronBag object either from a vector of query strings or a metadata data.frame.

Usage

neuronBag(
  typeQuery,
  fixed = FALSE,
  by.roi = TRUE,
  selfRef = FALSE,
  verbose = FALSE,
  omitInputs = FALSE,
  omitOutputs = FALSE,
  computeKnownRatio = FALSE,
  renaming = NULL,
  overruleThreshold = Inf,
  ...
)

Arguments

typeQuery	Either a vector of queries (similar to a getTypesTable queries) or a metadata data.frame for a set of neurons. If a data.frame it needs to contain all the instances of the types.
fixed	If typeQuery is a query string, is it fixed?
by.roi	Return results by ROI or just global weights?
selfRef	Deprecated argument
verbose	Inform about progress if TRUE
omitInputs	Skip calculation of inputs if TRUE
omitOutputs	Skip calculation of outputs if TRUE
computeKnownRatio	Computes relative weights and output contributions that sum to 1 (for types and for neurons). This requires keeping track of all the outputs of the inputs, and all the inputs of the outputs, in a field called ref
...	To be passed to getConnectionTable

Details

A neuronBag carries information about input and output connectivity of a group of neurons, at the neuron and type level, while keeping track of eventual type changes that occured. Particularly useful in combination with retyping functions. Methods exist for filtering (filter), concatenating (c) and all retyping utilities.

Value

An object of class neuronBag. The object is a list with fields:

names

A table of metadata associated with the neurons in the bag – with an extra column, 'databaseType' which keeps the type name used in the database.

outputs

A type to type connectivity table of the outputs of the set of neurons.

inputs

A type to type connectivity table of the inputs of the set of neurons.

outputs_raw

A neuron to neuron connection table of the outputs of the set of neurons.

inputs_raw

A neuron to neuron connection table of the inputs of the set of neurons.

outputsTableRef

A table holding all instances of all the output types and their associated metadata

See Also

lateralize_types, cxRetyping, redefine_types for retyping a bag.

jayaraman-lab/neuprintrExtra documentation built on Dec. 20, 2021, 10 p.m.