/ObMiTi

Primary LanguageR

ObMiTi

A MusMus Dataset of Ob/ob and WT mice on different diets.

Overview

In this document, we introduce the purpose of ObMiTi package, its contents and its potential use cases. This package is a dataset of RNA-seq samples. The samples are of 6 ob/ob mice and 6 wild type mice divided further into High fat diet and normal diet. From each mice 7 tissues has been analyzed. The duration of dieting was 20 weeks.

The package document the data collection, pre-processing and processing. In addition to the documentation the package contains the scripts that were used to generate the data in inst/scripts and access to the final RangedSummarizedExperiment object through ExperimentHub.

Introduction

What is ObMiTi?

It is an R package for documenting and distributing a dataset. The package doesn't contain any R functions.

What is contained in ObMiTi?

The package contains two different things:

  1. Scripts for documenting/reproducing the data in inst/scripts
  2. Access to the final RangedSummarizedExperiment through ExperimentHub.

What is ObMiTi for?

The RangedSummarizedExperiment object contains the counts, colData, rowRanges and metadata which can be used for the purposes of differential gene expression and get set enrichment analysis.

Installation

The ObMiTi package can be installed from Bioconductor using BiocManager.

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("ObMiTi")

Exploring the ob_counts object

In this section, we conduct a simple exploration of the data objects to show the content of the package and how they can be loaded and used.

# loading required libraries
library(ExperimentHub)
library(SummarizedExperiment)
library(dplyr)

# query package resources on ExperimentHub
eh <- ExperimentHub()
query(eh, "ObMiTi")

# load data from ExperimentHub
ob_counts <- query(eh, "ObMiTi")[[1]] 

# print object
ob_counts

Citing ObMiTi

For citing the package use:

#citing the package
citation("ObMiTi")