doPamClustering: Title

In kueckelj/celltracer: An Analysis-Toolbox for High-Throughput Cell Imaging Data

Description

Performs pam-clustering with the respective variables, during the denoted phase for all values denoted in input for argument k_values.

The name of the respective clustering results is assembled as a combination of 'pam_k' and the respective value for k.

Usage

doPamClustering(
  object,
  k_values,
  stand = TRUE,
  phase = "first_tmt",
  variables = "all",
  ...,
  verbose = TRUE
)

Arguments

object	A valid cell tracer object.
k_values	Numeric vector. Denotes all k-values of interest.
stand	Given to argument stand of function cluster::pam(). Denotes whether the numeric variables are scaled before the clsutering process or not. Default is TRUE.
phase	Character value. Refers to the phase of the experiment. Valid inputs are: 'before_tmt' Uses the data that refers to the time before the treatment. 'first_tmt' Uses the data that refers tot the time after the treatment. Note: This argument is ignored if the experiment set up did not include any treatment or the treatment started right from the beginning.
variables	The numeric variables upon which the clusters are calculated. Valid inputs can be obtained with the function getStatVariableNames(). The default is set to 'all' which includes all numeric values.
...	Additional arguments given to cluster::pam().
verbose	Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)

Value

An updated celltracer-object.

See Also

getPamObject(), getClusterNames()

kueckelj/celltracer documentation built on June 2, 2021, 6:37 a.m.