Compute dimensional reductions

Reduces the dimensions of all specified numeric variables using the respective algorithm.

runPca(
  object,
  variable_set,
  phase = NULL,
  force = FALSE,
  set_seed = NULL,
  verbose = NULL,
  ...
)

runTsne(
  object,
  variable_set,
  phase = NULL,
  force = FALSE,
  set_seed = NULL,
  verbose = NULL,
  ...
)

runUmap(
  object,
  variable_set,
  phase = NULL,
  force = FALSE,
  set_seed = NULL,
  verbose = NULL,
  ...
)

Arguments

object	A valid cypro object.
variable_set	Character value. Denotes the variable set of interest. Use getVariableSetNames() to obtain all names of currently stored variable sets in your object.
phase	Character or numeric. If character, the ordinal value referring to the phase of interest (e.g. 'first', 'second' etc.). referring to the phase of interest or 'all'. If numeric, the number referring to the phase. If set to NULL takes the phase denoted as default with adjustDefault(). Ignored if the experiment design contains only one phase.
force	Logical value. Needs to be set to TRUE if you want to overwrite an already existing set up or already existing results.
verbose	Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)
variables_subset	Character vector or NULL. Specifies the numeric variables the dimensional reduction algorithms will include. If set to NULL all of them are chosen. You can prefix variables you do NOT want to influence the clustering with a '-'. (Saves writing if there are more variables you are interested in than variables you are not interested in.) Use getNumericVariableNames() to obtain all valid input options.

Value

An updated version of the input cypro-object.