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cedricx edited this page Jul 9, 2019 · 5 revisions

Data

  • /cbica/projects/GURLAB/projects/xia_MSNR/data/original_data.RData
  • Organization:
  1. As.all: adjacency matrices for n=1051 subjects
  2. Xs.all: covariates for n=1051 subjects
  3. Ks: community assignment (p=236 Power264 without unassigned nodes)
  4. list.not.valid: combined training and testing sample (n = 813)
  5. list.valid: combined training and testing sample (n = 202)
  6. lists.train: a list of five vectors, each contains a training vector for 5-fold cross-validation
  7. lists.test:a list of five vectors, each contains a testing vector for 5-fold cross-validation

Code

  • /cbica/projects/GURLAB/projects/xia_MSNR/script/script
  • Organization:
MSNR code
  1. functions.R: script that contains the actual code for MSNR
run MSNR on original data
  1. org_par_fold.R: script performs one five-fold cross-validation of MSNR on the data. Here you need to change serverDir,workingdir,outdir, and save the result section as appropriate to your project. lam1.vals and lam2.vals control the search parameter space. Additionally, to select n=150, set this up in the code blocks assemble data and generate sets. See an example below.
  2. 'org_par_fold_job_submit.sh': _Here you need to change logFile,codeDir as appropriate to your project.
run MSNR on permuted data
  1. perm_par_fold.R: script performs one five-fold cross-validation of MSNR on the data. Here you need to change serverDir,workingdir,outdir, and save the result section as appropriate to your project. lam1.vals and lam2.vals control the search parameter space. Additionally, to select n=150, set this up in the code block assemble data and generate sets.
  2. 'perm_par_fold_job_submit.sh': _Here you need to change logFile,codeDir as appropriate to your projlsect. ######## example to select 150 for prototyping ######## As.train = As.not.valid[lists.train[[f]][1:100],,] As.test = As.not.valid[lists.test[[f]][1:50],,]