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backtobaseidentifiers.qmd
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backtobaseidentifiers.qmd
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---
title: "To base identifiers"
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:** [BackToBaseIdentifiers.cs](https://github.com/JurgenCox/perseus-plugins/blob/master/PerseusPluginLib/AnnotCols/BackToBaseIdentifiers.cs)
# Brief description
This activity does the inverse of the [Add annotation](addannotationtomatrix.html) activity. Any of the columns that can be created by the [Add annotation](addannotationtomatrix.html) activity can be mapped back to the base identifiers (typically UniProt ids).
```{=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 mapped back to the base identifiers (default: first file in Perseus-version `/conf/annotations/`). The file should be the same that was used to add the annotations, also it can be selected from all files in Perseus-version `/conf/annotations/`.
## Identifiers
Selected text column containing the identifiers that should be matched back to UniProt identifiers (default: first text column in the matrix).
**Comment:** Only text columns can be matched back **not** categorical ones, because there is no unique match.
## Identifier type
Selected type of the identifiers that will be mapped back (default: Gene name). The identifier type can be selected from a predefined list:
- ENSG
- ENSP
- ENST
- Flybase
- Gene name
- MGI
- PDB
- UniProt names
- Wormbase
- EC
- eggNOG
==== Parameter window
![](images/modifications-to_base_identifiers-edited.png)