This package contains functions that scrape MitoCarta3.0 data from the web for easy assignment of a pre-defined list of genes to the mitochondrial pathways identified by MitoCarta, including systematic checking of MitoCarta gene names synonyms. This package also provides a function to plot the percent of each pathway that is represented in a filtered gene list or cluster of genes.
The functions, data, and .Rmd workflow herein are a companion to the following article:
Fleischman, J. Y., Van den Bergh, F., Collins, N. L., Bowers, M., Beard, D. A., & Burant, C. F. (2023). Higher mitochondrial oxidative capacity is the primary molecular differentiator in muscle of rats with high and low intrinsic cardiorespiratory fitness. In Molecular Metabolism (Vol. 76, p. 101793). Elsevier BV. https://doi.org/10.1016/j.molmet.2023.101793
This package is not frequently updated. Please contact the author for help or to address bugs.
First, download and install R and RStudio:
Then, open RStudio and install the devtools package
install.packages("devtools")
Finally, install the MitochondrialGeneAnalysis package
library(devtools)
devtools::install_github("johanna0321/MitochondrialGeneAnalysis")
The following are included in the package and documentation is accessible using the help() function or ? help operator
Data:
expected.counts
expected.counts.meta
gene_name_conversion
Functions:
extract_mitocarta_pathways()
check_mitocarta_synonyms()
assign_mitocarta_pathways()
plot_mitocarta_pathways()