R-functions

Content:

1. Regeneration: Collapse replicates by mean
2. Functions to manage GTF files
3. mRNA-lncRNA pair plots
4. Generate time point plot
5. Handle excel Alternative Splicing events
6. Pairwise Correlation analysis
7. PCA specific samples
8. Plot Correlation
9. Remove Batch effect
10. tSNE specific samples
11. FEELnc utilities
12. bioMaRt example

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

6) PCA specific samples

7) Plot Correlation

8) Remove Batch effect

9) tSNE specific samples

10) FEELnc utilities

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