README.md

In Mengbo-Li/brainClass: Transcriptional Data Guided fMRI Network Classification

brainClass: Transcriptional-data-guided brain network classification

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.

Installation

To install the package, use the following script in R:

# install.packages("devtools")
devtools::install_github("Mengbo-Li/brainClass")

Data

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.

Penalised group lasso algorithms

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.

Analysis pipeline

See vignettes for the standard workflow with brainClass.

Contact

Open an issue or email me at [e-mail].

Mengbo-Li/brainClass documentation built on March 16, 2023, 12:06 p.m.