# MPLasso
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File: README.md
A brief introduction about the usage for MPLasso
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Author: Chieh Lo (Carnegie Mellon University)
Email : chiehl@andrew.cmu.edu
Date : 2017-03-22
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Files:
./Demo_Synthetic.R: A demo for synthetic datasets.
./Demo_HMP.R: A demo for HMP datasets.
./R/algorithm.R: Implementation of the MPLasso
./R/calculate_co_occurrence.R: Calculate the prior information based on microbial co-occurrence.
./R/evaluation.R: Evaluate the performacne of the MPLasso.
./R/normalization.R: Log-ratio transformation for microbial data.
./R/real_data.R: HMP data preprocessing.
./R/selection.R: Model selection for MPLasso based on BIC.
./R/syn_data_generate.R: Generation of synthetic data of five different graphs using huge package.
HMP datasets:
./data/HMASM/: Post-processing count data and the prior information obtained using @MInter.
./data/HMMCP/: Post-processing count data and the prior information obtained using @MInter
./data/HMQCP/: Post-processing count data and the prior information obtained using @MInter
For HMASM, it includes both species interactions and co-occurrance prior information.
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Quick start:
source Demo_Synthetic.R or Demo_HMP.R in Rstudio.