GitHub - tyeulalio/regionalpcs (original) (raw)

regionalpcs

Table of Contents

  1. Introduction
  2. Repository Contents
  3. System Requirements
  4. Installation Guide
  5. Demo

Introduction

Tiffany Eulalio

The regionalpcs package aims to address the challenge of summarizing and interpreting DNA methylation data at a regional level. Traditional methods of analysis may not capture the biological complexity of methylation patterns, potentially leading to less accurate or less meaningful interpretations. This package introduces the concept of regional principal components (rPCs) as a tool for capturing more biologically relevant signals in DNA methylation data. By using rPCs, researchers can gain new insights into complex interactions and effects in methylation data that might otherwise be missed.

Repository Contents

System Requirements

Hardware Requirements

The regionalpcs package is designed to function efficiently on a standard computer setup. The specific RAM requirement depends on the scale of the analysis defined by the user. Below are our recommendations for minimal and optimal performance configurations:

Runtime Benchmarks: The reported runtimes are based on tests conducted on a system equipped with 64 GB RAM, an 8-core CPU @ 3.60 GHz, and an internet connection speed of 229 Mbps.

Software Requirements

Operating System Compatibility

While the development version of the regionalpcs package is primarily tested on Windows platforms, we aim for broad compatibility across major operating systems.

Our Bioconductor packageregionalpcshas been tested with Windows, Mac, and Linux operating systems. Here are the details regarding the tested systems:

R and Package Dependencies

To install and run the regionalpcs package, the following software requirements must be met:

dplyr PCAtools tibble GenomicRanges

Please refer to the package documentation for a detailed list of dependencies and instructions for setting up the required software environment.

Installation Guide

You can install the regionalpcs package from Bioconductor using the following command:

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

BiocManager::install("regionalpcs")

which will install in about 30 seconds on a machine with the recommended specs.

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

install devtool package if needed

if (!requireNamespace("devtools", quietly=TRUE)) install.packages("devtools")

download the regionalpcs package

devtools::install_github("tyeulalio/regionalpcs")

Demonstration

Explore the functionalities of the regionalpcs package with our interactive tutorials provided as vignettes. These vignettes offer step-by-step guidance on using the package’s main features and are designed to help you get started quickly.

Accessing the Vignettes

To start the tutorials, ensure that the regionalpcs package is installed and loaded into your R session. You can then access the vignettes directly in R with the following commands:

Load the regionalpcs package

library(regionalpcs)

Open the main vignette

vignette('regionalpcs-introduction')

Online Access

Alternatively, for access to a browser-friendly version, visit theregionalpcs Bioconductor page. Here, you’ll find the vignettes available in HTML and R formats.

Tutorial Duration

The primary vignette is concise and informative, designed to provide a comprehensive overview within approximately 20 seconds. This makes it an efficient way to familiarize yourself with the package’s capabilities and start applying them to your data analysis projects.

Session Information

sessionInfo() #> R version 4.3.1 (2023-06-16 ucrt) #> Platform: x86_64-w64-mingw32/x64 (64-bit) #> Running under: Windows 10 x64 (build 19045) #> #> Matrix products: default #> #> #> locale: #> [1] LC_COLLATE=English_United States.utf8 #> [2] LC_CTYPE=English_United States.utf8
#> [3] LC_MONETARY=English_United States.utf8 #> [4] LC_NUMERIC=C
#> [5] LC_TIME=English_United States.utf8
#> #> time zone: America/Los_Angeles #> tzcode source: internal #> #> attached base packages: #> [1] stats graphics grDevices utils datasets methods base
#> #> loaded via a namespace (and not attached): #> [1] compiler_4.3.1 fastmap_1.1.1 cli_3.6.1 tools_4.3.1
#> [5] htmltools_0.5.6 rstudioapi_0.16.0 yaml_2.3.7 rmarkdown_2.26
#> [9] knitr_1.46 xfun_0.43 digest_0.6.33 rlang_1.1.1
#> [13] evaluate_0.23