Calculates a (weighted) self-organizing map

Source: R/dimension_reduction.R

Calculates a (weighted) self-organizing map

scSOM(object, exprs_values = "norm_TPM", features = NULL, scale = T,
  num_epochs = 200, resolution = 1, seed = NULL, init = NULL,
  init.FUN = map.init, ...)

Arguments

object

A SingleCellExperiment object.
exprs_values

String indicating which assay contains the data that should be used to perform SOM calculation.
features

A character vector (of feature names), a logical vector or numeric vector (of indices) specifying the features to use for SOM calculation. The default of NULL will use all features.
scale

Logical scalar indicating whether data should be scaled before SOM calculation.
num_epochs

How long the training should last.
resolution

A multiplier for the map size.
seed

A numeric seed to initialize the random number generator.
init

A list with initialization parameters.
init.FUN

A function to initialize the map.
...

Additional arguments passed to som.

Value

A som object.