doubledeepms: doubledeepms

In lehner-lab/doubledeepms: Analysis scripts to reproduce the figures and results from doubleDeepPCA manuscript

doubledeepms

Description

Main analysis script.

Usage

doubledeepms(startStage = 1, stopStage = 15,
  base_dir = "/users/project/prj004631/afaure/DMS/Results/doubledeepms_proj",
  tmodel_job_number = 1, tmodel_grid_search = FALSE,
  tmodel_protein = "GRB2-SH3", tmodel_subset = 100)

Arguments

startStage	Start at a specified analysis stage (default:1)
stopStage	Stop at a specified analysis stage (default:15)
base_dir	Base directory for all output files (default:NB private CRG server path; change accordingly)
tmodel_job_number	Thermodynamic model fit job number: 1:final model, 2-11: monte carlo simluations for confidence intervals of model-inferred free energies (default:1)
tmodel_grid_search	Thermodynamic model fit grid search to determine optimal hyperparameters (default:FALSE)
tmodel_protein	Thermodynamic model fit proteins: comma-separated list of names or 'all' (default:'GRB2-SH3')
tmodel_subset	Thermodynamic model fit data subset: either an integer percentage of subsampled doubles (1-100) or "binding_only" or "singles_only" (default:100)

Value

Nothing

lehner-lab/doubledeepms documentation built on July 21, 2023, 4:10 a.m.