removeOutliers: Remove outliers from object

In theMILOlab/cypro: A Toolbox for Analysis of Single Cell Microscopy Data

Remove outliers from object

Description

Removes the data from the cell ids detected by detectOutliers() from the object. As this changes the data set all clustering-, correlation- and dimensional reduction results are reset.

Usage

removeOutliers(
  object,
  method_outlier,
  new_name = "outlier_removed",
  phase = NULL,
  verbose = NULL
)

Arguments

object	A valid cypro object.
method_outlier	Character vector. Specifies the method/algorithm of interest. Use validOutlierDetectionMethods() to obtain all valid input options.
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.
verbose	Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)

Details

Cell are removed via a reversed application of subsetByCellId(). You can therefore keep track of conducted outlier removal by using function printSubsetHistory() which prints summary text on how, when and why you subsetted the cypro object.

Value

An updated version of the input cypro-object.

See Also

detectOutliers()

theMILOlab/cypro documentation built on April 5, 2022, 2:03 a.m.