Filter rows based on valid values

Author

Cox Lab

Published

March 18, 2024

1 General

2 Brief description

Rows of the expression matrix are filtered to contain at least the specified numbers of entries that are valid in the specified way.

Output: The matrix of expression values is constrained to contain only these rows that fulfill the requirement.

3 Parameters

3.1 Min. number of values

Defines the minimal number of valid values each row needs to have in the expression columns to survive the filtering process (default: 3).

3.2 Mode

Defines, which expression columns are counted to define, if a row has enough valid values to survive the filtering process (default: In total). There are three options available:

  • In total (includes all expression columns)
  • In each group
  • In at least one group

3.2.1 Grouping

This parameter is just relevant, if Mode (Section 3.2) is set to “In each group” or “In at least one group”. It defines the grouping of the expression columns that should be used by selecting a categorical row (default: first categorical row of the matrix).

3.3 Values should be

Defines the restriction for a value to be classified as valid (default: Valid). There are seven different possibilities to specify, which entry is counted as a valid value (default: Valid):

  • Valid
  • Greater than
  • Greater or equal
  • Less than
  • Less or equal
  • Between
  • Outside

3.3.1 Minimum

This parameter is just relevant, if “Values should be” is set to “Greater than”, “Greater or equal”, “Between” or “Outside”. It defines a lower bound to apply the operation specified in “Values should be” (default: 0).

3.3.2 Maximum

This parameter is just relevant, if “Values should be” is set to “Less than”, “Less or equal”, “Between” or “Outside”. It defines a upper bound to apply the operation specified in “Values should be” (default: 0).

3.4 Filter mode

The “Filter mode” defines, whether the input matrix will be reduced (“Reduce matrix” = default) or a new categorical column called “Filter” will be generated containing the categories “Keep” and “Discard” (“Filter mode” = “Add categorical column”).

4 Parameter window