multiOmicDataSet object class for MOSuite

MOObject defines the multiOmicDataSet object class which is used in MOSuite for differential RNA-seq and multi-omics analyses. Separating the MOObject class definition from MOSuite allows for lightweight installations in downstream workflows. See the MOObject website for more information about the class, and see the MOSuite website for the most in-depth discussion about using these packages.

Installation

You can install the development version of MOObject from GitHub with:

# install.packages("remotes")
remotes::install_github("CCBR/MOObject")

Or install a specific version:

remotes::install_github("CCBR/MOObject", dependencies = TRUE, ref = "v0.5.0")

Usage

MOObject

If you only need to read and write multiOmicDataSet objects, MOObject is the package you should use to minimize dependencies for your project.

MOObject responsibilities:

Define and export the S7 class multiOmicDataSet.
Implement object-focused helpers only: constructors, validators, readers, and writers.
Keep dependencies minimal (prefer base + S7 + lightweight IO packages only).

library(MOObject)

# create from csv files.
# example data are included in the MOSuite package.
base_url <- paste0(
  "https://raw.githubusercontent.com/CCBR/MOSuite/",
  "refs/tags/v0.4.2/inst/extdata/nidap/"
)
sample_meta_filepath <- paste0(
  base_url,
  "Sample_Metadata_Bulk_RNA-seq_Training_Dataset_CCBR.csv.gz"
)
feature_counts_filepath <- paste0(base_url, "Raw_Counts.csv.gz")

moo <- create_multiOmicDataSet_from_files(
  sample_meta_filepath,
  feature_counts_filepath
)

# write to Rds
moo |> write_multiOmicDataSet(filepath = 'moo.rds')
# write individual components to separate files in a directory
moo |> write_multiOmicDataSet_properties(output_dir = 'moo')

# read from Rds
moo <- read_multiOmicDataSet('moo.rds')

View the reference for a comprehensive list of functions exported by MOObject.

MOSuite

MOSuite is the main package containing method implementations for bulk-RNA-seq and multi-omics analysis. Please see the introductory vignette for a quick start tutorial, or take a look at the reference documentation for detailed information on each function in the package.

MOSuite depends on MOObject and wraps its functions, so if you’re already using MOSuite, you already have access to everything available in MOObject

library(MOSuite)
moo <- read_multiOmicDataSet('moo.rds')

MOSuite responsibilities:

Define functions for analysis, modeling, plotting, normalization, filtering, and reporting.
Import and operate on multiOmicDataSet from MOObject.

Help & Contributing

Come across a bug? Open an issue and include a minimal reproducible example.

Have a question? Ask it in discussions.

Want to contribute to this project? Check out the contributing guidelines.

MOObject 🐮