MotrpacRatTraining6moData

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Table of Contents

• Overview
  • About this package
  • About MoTrPAC
• Installation
  • Troubleshooting
  • Last resort
• Explore available data objects
• Access epigenomics data through Google Cloud Storage
• Getting help
• Acknowledgements
• Licenses
• Citing MoTrPAC data

Overview

About this package

This package provides convenient access to the processed data and downstream analysis results presented in the main paper for the first large-scale multi-omic multi-tissue endurance exercise training study conducted in young adult rats by the Molecular Transducers of Physical Activity Consortium (MoTrPAC). Find the open access manuscript published in Nature. See the vignette for examples of how to use this package.

While the data in this package can be used by themselves, the MotrpacRatTraining6mo R package relies heavily on this package and provides many functions to help retrieve and explore the data. See examples in the MotrpacRatTraining6mo vignette.

About MoTrPAC

MoTrPAC is a national research consortium designed to discover and perform preliminary characterization of the range of molecular transducers (the "molecular map") that underlie the effects of physical activity in humans. The program's goal is to study the molecular changes that occur during and after exercise and ultimately to advance the understanding of how physical activity improves and preserves health. The six-year program is the largest targeted NIH investment of funds into the mechanisms of how physical activity improves health and prevents disease. See motrpac.org and motrpac-data.org for more details.

Installation

Install this package with devtools:

if (!require("devtools", quietly = TRUE)){
  install.packages("devtools")
}
options(timeout=1e5) # extend the timeout
devtools::install_github("MoTrPAC/MotrpacRatTraining6moData")

The output for a successful installation looks something like this. Note that the *** moving datasets to lazyload DB step takes the longest (~5 minutes):

Downloading GitHub repo MoTrPAC/MotrpacRatTraining6moData@HEAD
✓  checking for file ‘.../MoTrPAC-MotrpacRatTraining6moData-1c6478a/DESCRIPTION’ ...
─  preparing ‘MotrpacRatTraining6moData’:
✓  checking DESCRIPTION meta-information
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘MotrpacRatTraining6moData_1.3.2.tar.gz’ (1.3s)
   
* installing *source* package ‘MotrpacRatTraining6moData’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MotrpacRatTraining6moData)

Troubleshooting

If you get this error after setting options(timeout=1e5):

Downloading GitHub repo MoTrPAC/MotrpacRatTraining6moData@HEAD
Error in utils::download.file(url, path, method = method, quiet = quiet,  : 
  download from 'https://api.github.com/repos/MoTrPAC/MotrpacRatTraining6moData/tarball/HEAD' failed
Error in `action()`:
! `class` is absent but must be supplied.
Run `rlang::last_error()` to see where the error occurred.

...this seems to be an intermittent issue seen only on Mac, not Linux or Windows. This was resolved by installing the newest version of R.

Last resort

If you can't get devtools::install_github("MoTrPAC/MotrpacRatTraining6moData") to work, try this:

1. Go to https://api.github.com/repos/MoTrPAC/MotrpacRatTraining6moData/tarball/HEAD, which will automatically start downloading this repository in a tarball
2. Install the package from source:

   install.packages("~/Downloads/MoTrPAC-MotrpacRatTraining6moData-0729e2e.tar.gz", 
     repos = NULL, 
     type = "source")
   library(MotrpacRatTraining6moData)
   

Explore available data objects

Find the index of available objects here. Click on the name of an object in this index to see its documentation.

Alternatively, explore data objects in R:

# load the package
library(MotrpacRatTraining6moData)

# list available objects
data(package = "MotrpacRatTraining6moData")

# get the documentation for a given data object
?TRNSCRPT_LIVER_DA

# load a data object into your environment using `data()`
data(TRNSCRPT_LIVER_DA)
# or just use it directly, e.g., 
head(TRNSCRPT_LIVER_DA)

Access epigenomics data through Google Cloud Storage

Due to file size, only normalized sample-level data and differential analysis results corresponding to training-regulated features (5% IHW FDR) are contained in this package for chromatin accessibility (ATAC) and DNA methylation (METHYL). The full sets of epigenetic results may be downloaded either with R functions in the MotrpacRatTraining6mo package or through the following public URLs.

Note that clicking on a Link automatically starts a download. To instead copy the URL for an object, right-click the Link and select Copy Link Address.

To download and load epigenetic data within R, use one of the following functions in the MotrpacRatTraining6mo package:

• load_sample_data(): For sample-level data from a single tissue and ome.
• combine_normalized_data(): For sample-level data from multiple tissues or omes. Use include_epigen = TRUE.
• combine_da_results(): For differential analysis results from multiple tissues or omes. Use include_epigen = TRUE.
• Several other functions specifically for loading epigenetic data are documented here.

Note that the size in this table is the compressed size. Each object occupies several times more memory when loaded into R. The total compressed size for all of these objects is 8.68 GiB (~9.32 GB).

Type|Assay|Tissue|Object|Size (MiB)|Click to download| ---|---|---|---|---|---| Differential analysis results|ATAC|BAT|ATAC_BAT_DA|329.71|Link Differential analysis results|ATAC|HEART|ATAC_HEART_DA|238.99|Link Differential analysis results|ATAC|HIPPOC|ATAC_HIPPOC_DA|223.06|Link Differential analysis results|ATAC|KIDNEY|ATAC_KIDNEY_DA|272.7|Link Differential analysis results|ATAC|LIVER|ATAC_LIVER_DA|202.48|Link Differential analysis results|ATAC|LUNG|ATAC_LUNG_DA|259.19|Link Differential analysis results|ATAC|SKM-GN|ATAC_SKMGN_DA|320.42|Link Differential analysis results|ATAC|WAT-SC|ATAC_WATSC_DA|359.23|Link Normalized sample-level data|ATAC|BAT|ATAC_BAT_NORM_DATA|43.11|Link Normalized sample-level data|ATAC|HEART|ATAC_HEART_NORM_DATA|31.34|Link Normalized sample-level data|ATAC|HIPPOC|ATAC_HIPPOC_NORM_DATA|33.52|Link Normalized sample-level data|ATAC|KIDNEY|ATAC_KIDNEY_NORM_DATA|40.03|[Link](https://storage.googleapis.c