Transcriptional-data-guided brain network classification that links the brain connectome to the brain transcriptome. Processed example data included. See https://www.biorxiv.org/content/10.1101/2020.05.15.099028v1 for details.
To install the package, use the following script in R:
# install.packages("devtools")
devtools::install_github("Mengbo-Li/brainClass")
Processed COBRE and UMich fMRI network data are obtained from the graphclass package. See graphclass.pdf for details and references.
The whole brain gene expression data are publicly available from the Allen Human Brain Atlas (AHBA). Processed AHBA samples are summarised into the region-of-interest (ROI) level, where ROIs are defined by the Power Parcellation. Corrected MNI coordinates of the AHBA wells are obtained from chrisgorgo/alleninf.
Data references:
Aine, C. J., Bockholt, H. J., Bustillo, J. R., Cañive, J. M., Caprihan, A., Gasparovic, C., ... & Calhoun, V. D. (2017). Multimodal neuroimaging in schizophrenia: description and dissemination. Neuroinformatics, 15(4), 343-364.
Hawrylycz, M. J., Lein, E. S., Guillozet-Bongaarts, A. L., Shen, E. H., Ng, L., Miller, J. A., ... & Jones, A. R. (2012). An anatomically comprehensive atlas of the adult human brain transcriptome. Nature, 489(7416), 391-399.
Kim, J., So, S., Lee, H. J., Park, J. C., Kim, J. J., & Lee, H. (2013). DigSee: disease gene search engine with evidence sentences (version cancer). Nucleic acids research, 41(W1), W510-W517.
Liberzon, A., Subramanian, A., Pinchback, R., Thorvaldsdóttir, H., Tamayo, P., & Mesirov, J. P. (2011). Molecular signatures database (MSigDB) 3.0. Bioinformatics, 27(12), 1739-1740.
Power, J. D., Cohen, A. L., Nelson, S. M., Wig, G. S., Barnes, K. A., Church, J. A., ... & Petersen, S. E. (2011). Functional network organization of the human brain. Neuron, 72(4), 665-678.
Relión, J. D. A., Kessler, D., Levina, E., & Taylor, S. F. (2019). Network classification with applications to brain connectomics. The annals of applied statistics, 13(3), 1648.
The brainClass package uses the grpregOverlap::grpregOverlap algorithm for penalised logistic regression with (user-defined) overlapping feature (covariate) groups. The GitHub page of the grpregOverlap package is here.
See vignettes for the standard workflow with brainClass.
Open an issue or email me at mengboli103@gmail.com.