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addannotationtomatrix.qmd
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addannotationtomatrix.qmd
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---
title: "Add annotation"
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:** - Annot. columns
- **Source code:** [AddAnnotationToMatrix.cs](https://github.com/JurgenCox/perseus-plugins/blob/master/PerseusPluginLib/AnnotCols/AddAnnotationToMatrix.cs)
# Brief description
Based on a column containing protein (or gene or transcript) identifiers this activity adds columns with annotations. These are read from specifically formatted files contained in the folder `conf/annotations` in your Perseus installation. Species-specific annotation files generated from UniProt can be downloaded from the link specified in the menu at the blue box in the upper left corner.
```{=html}
<!-- This comment and the line above it must be preserved when editing this file!
The recommended sections are these, but they may be changed on a case by case basis.
===== Detailed description =====
===== Parameters =====
===== Theoretical background =====
===== Examples =====
Make changes only below this line! -->
```
# Parameters
## Source
Specified path to the file containing the annotations that should be added to the matrix (default: first file in Perseus-version `/conf/annotations/`). The file can be selected from all files in Perseus-version `/conf/annotations/`.
### ENSG column
Selected text column that contains the base identifier, which are going to be matched to the annotations (default: first text column in the matrix).
### Annotations to be added
Selected annotations that should be added (default: no annotations are selected). The annotations can be selected from a list of annotations defined by the tab separated columns in the file specified in "Source".
## Additional sources
Selected files containing the annotations that should additionally be added to the matrix (default: no files are selected). Additional sources can be selected from all files in Perseus-version `conf/annotations`.
# Parameter window
![](images/annot-columns-add_annotations-edited.png)