filtervalidvaluesrows.qmd

---
title: "Filter rows based on valid values"
author: "Cox Lab"
format: 
  html:
    toc: true
    toc-depth: 4
    toc-expand: false
    number-sections: true
    number-depth: 4
editor: source
date: today
bibliography: references.bib
---

# General

-   **Type:** - Matrix Processing
-   **Heading:** - Filter rows
-   **Source code:** [FilterValidValuesRows.cs](https://github.com/JurgenCox/perseus-plugins/blob/master/PerseusPluginLib/Filter/FilterValidValuesRows.cs)

# 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.

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# Parameters

## 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).

## Mode {#sec-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

### Grouping

This parameter is just relevant, if Mode (@sec-mode) 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).

## 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

### 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).

### 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).

## 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").

# Parameter window

![](images/filter_rows-filter_rows_based_on_valid_values-edited.png)