Mimir package

R package to create metadata profiles for CLIP and other types of NGS data.

Table of Content

Installation Instructions
Documentation
- Basic Example
Bugs and Issues
License

Installation Instructions

Prerequisities

R (>=3.6.0) with a working version of Bioconductor. Although the package has not been tested with previous versions of R, it might still work.
Required dependencies will be installed via BiocManager:install().

Install Repository

Install and load the devtools package:

install.packages("devtools")
library(devtools)

Install the fagostini/Mimir package:

install_github("fagostini/Mimir", type = "source", repos = BiocManager::repositories(), dependencies = TRUE)

Install Package Release

Download the latest source release from here and install it:

install.packages(path_to_file, type = "source", repos = BiocManager::repositories(), dependencies = TRUE)

Documentation

Coming soon...

Basic Example

This basic example shows how to extract the genomic features (i.e., the genes, with their upstream and downstream regions) from a TxDb object

# Load the package
library("Mimir")

# Load a pre-compiled TxDb object
library("TxDb.Dmelanogaster.UCSC.dm3.ensGene")

txdb = TxDb.Dmelanogaster.UCSC.dm3.ensGene

# Extract the genomic features
query = extractGenomicFeatures(TxDb = txdb)

Extracted 10562 genes

Extracted 10559 upstream regions

Extracted 10562 downstream regions

Now that the regions have been extracted, the signal across these features can be calcualted

# Load sample Bam files and packages to read them 
library("GenomicAlignments")
library("pasillaBamSubset")

# Locate and read the alignemnt file
fl1 <- untreated1_chr4()
subject = readGAlignments(fl1)

# Create the profiles across the regions
profile = profileGenomicFeatures(genomicRegions = query, sampleObject = subject, TxDb = txdb)

Upstream regions on + strand: 5261

Upstream regions on - strand: 5298

Gene_body regions on + strand: 5264

Gene_body regions on - strand: 5298

Downstream regions on + strand: 5264

Downstream regions on - strand: 5298

Finally, the profile obtained can be visualised

# Load the plotting package
library("ggplot2")

# Plot the profiles
ggplot(profile, aes(x=bin, y=Mean, colour=region_id)) + 
   geom_line() +
   geom_vline(xintercept=c(50.5, 150.5), linetype="dashed", colour="grey30") +
   scale_x_continuous("Relative position",
        breaks=c(1, 50.5, 150.5, 250), label=c("-500", "TSS", "TES", "1000")) +
   scale_y_continuous("Average normalised signal") +
   coord_cartesian(xlim=c(0, 250)) +
   theme_bw() +
   theme(legend.position=c(0.9, 0.8), legend.background=element_blank()) +
   guides(colour=guide_legend(title=""))

Bugs and Issues

Report bugs as issues on the GitHub repository

License

This project is licensed under the MIT License - see the LICENSE file for details

License

fagostini/Mimir

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