https://github.com/razielar/r-functions
https://github.com/razielar/r-functions
Last synced: 3 months ago
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- Host: GitHub
- URL: https://github.com/razielar/r-functions
- Owner: razielar
- License: mit
- Created: 2019-01-31T10:39:18.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2021-08-20T08:59:58.000Z (almost 4 years ago)
- Last Synced: 2025-01-11T14:48:37.689Z (4 months ago)
- Language: R
- Size: 253 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# R-functions
### Content:
1. [Regeneration: Collapse replicates by mean](#mean)
2. [Functions to manage GTF files](#gtf)
3. [mRNA-lncRNA pair plots](#lncRNAmRNA)
3. [Generate time point plot](#time_plot)
4. [Handle excel Alternative Splicing events](#excel)
5. [Pairwise Correlation analysis](#cor)
6. [PCA specific samples](#pca)
7. [Plot Correlation](#plot_cor)
8. [Remove Batch effect](#batch)
9. [tSNE specific samples](#tsne)
10. [FEELnc utilities](#id_names)
11. [bioMaRt example](#biomart)
## 1) Collapse replicates by mean
To use the script: *Regeneration/f.Collapse.Regeneration.replicates.by.mean.R* the input matrix has to have the following order otherwise the mean calculations are senseless. Matrix order:
* Control_0h_R1_India
* Control_0h_R2_India
* Regeneration__0h_R1_India
* Regeneration__0h_R2_India
* Control_15h_R1_India
* Control_15h_R2_India
* Regeneration__15h_R1_India
* Regeneration__15h_R2_India
* Control_25h_R1_India
* Control_25h_R2_India
* Regeneration__25h_R1_India
* Regeneration__25h_R2_India
## 2) Functions to manage GTF files
## 3) mRNA-lncRNA pair plots
Script: *f.lncRNA.mRNA.pair.Generate.plot.R*
Description:
This function needs 2 inputs:
1. Expression matrix (Gene_IDs in rows and Sample_Names in columns)
2. lncRNA-mRNA pais in the following **order**:
| lncRNA_Gene_ID | lncRNA_Gene_Name | mRNA_Gene_ID | mRNA_Gene_Name |
|----------|:-------------:|------:| ------:|
| FBgn0058469 | CR40469 | FBgn0025837 | CG17636 |
| FBgn0266686 | CR45176 | FBgn0036992 | CG11796 |
| FBgn0267913 | CR46194 | FBgn0014184 | Oda |
## 3) Generate time point plot
## 4) Handle exel Alternative Splicing events
## 5) Pairwise Correlation analysis
### 10.1) Change Gene_ID into Gene_Name
Description:
This function converts FEELnc classification output from gene IDs into gene names (*and transcripts*). By default it doesn't maintain lncRNA IDs (*maintain.ID = FALSE*)
This function needs 3 inputs:
* **1)** FEELnc_classification output with *default order* (isBest, lncRNA_gene, lncRNA_transcript, partnerRNA_gene, partnerRNA_transcript, direction, type, distance, subtype, location)
* **2)** lncRNA gene description: Gene_ID, Gene_Name, Transcript_ID and Transcript_Name
* **3)** mRNA genes description: sames as lncRNA.
### 10.2) Obtain lincRNA with lowest distance
Obtain the long intergenic RNA (lincRNA) with the lowest distance with its partner mRNA or another genomic feature (*promoter, etc.*) and if all lincRNA-mRNA pairs have the same distance maintain the first one (this is arbitrary).
## 11) bioMaRt example using *Dme*:
Script: *bioMart.example.dme.R*
Description:
In this script some examples are presented on how to use bioMaRt to retrieve genomic information using *Dme*