Filter columns based on valid values

Author

Cox Lab

Published

November 15, 2023

1 General =====

2 Brief description

Columns 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 columns that fulfill the requirement.

3 Parameters

3.1 Min. number of values

Specifies minimal number of valid values each expression column needs to contain 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).

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