LLRC Runner

This program uses LLRC to compute QCDM values using QC metric values from Quameter and SMAQC (Software Metrics for Analysis of Quality Control)

Requirements

You must install the LLRC library into R prior to running LLRC. Steps:

1. Install R R-4.x (for example, R-4.1.1)

• Use defaults (core, 32-bit, and 64-bit)

2. Install the glmnet package

• Start R

  • Either use the GUI
  • Or start via the command line:
    • C:\Program Files\R\R-4.1.1\bin\x64\R.exe

• Install the package

  • > install.packages(c("glmnet"), repos='https://cran.revolutionanalytics.com/')

• Exit R

  • > quit()

3. Install QCDM_2020.05.04.tar.gz into R

• Option 1: use the command prompt

  • "C:\Program Files\R\R-4.1.1\bin\R.exe" CMD INSTALL QCDM_2020.05.04.tar.gz
  • If you see a permissions error, update the permissions on C:\Program Files\R\R-4.1.1\library as discussed above

• Option 2: use the GUI

  • Start the 64-bit R GUI
  • Choose Packages, then "Install packages from local zip file"
  • Choose file QCDM_2020.05.04.tar.gz
  • If prompted "Would you like to use a personal library instead?", choose "No"
    • Next, update "C:\Program Files\R\R-4.1.1\library" to grant "Write" access (you only need "Write", not "Modify")
    • Now try again with menu item "Install packages from local zip file"

Console Switches

Syntax:

LLRCRunner.exe
   DatasetIDList [/W:WorkingDirectory] 
   [/DB] [/Skip]

DatasetIDList can be a single DatasetID, a list of DatasetIDs separated by commas, a range of DatasetIDs separated with a dash, or a timespan in hours. Examples:

Command	Description
LLRCRunner.exe 325145	Process a single dataset
LLRCRunner.exe 325145,325146,325150	Process 3 datasets
LLRCRunner.exe 325145-325150	Process a range of 6 datasets
LLRCRunner.exe 24h	Process all "new" datasets added to DMS in the last 24 hours

"New" datasets are those with null QCDM values in the T_Dataset_QC table

Use /W to specify the working directory path

• The default is the directory with the .exe
• The working directory must have files Models_paper.Rdata and allData_v4.Rdata

Use /DB to post the LLRC results to the database

• Calls stored procedure StoreQCDMResults

Use /Skip to skip datasets that already have a QCDM value defined

Contacts

Written by Joshua Davis and Matthew Monroe for the Department of Energy (PNNL, Richland, WA)
E-mail: [email protected] or [email protected]
Website: https://github.com/PNNL-Comp-Mass-Spec/ or https://www.pnnl.gov/integrative-omics

License

The LLRC Runner is licensed under the 2-Clause BSD License; you may not use this program except in compliance with the License. You may obtain a copy of the License at https://opensource.org/licenses/BSD-2-Clause

Copyright 2023 Battelle Memorial Institute