This program uses LLRC to compute QCDM values using QC metric values from Quameter and SMAQC (Software Metrics for Analysis of Quality Control)
You must install the LLRC library into R prior to running LLRC. Steps:
- Install R R-4.x (for example, R-4.1.1)
- Use defaults (core, 32-bit, and 64-bit)
- 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()
- 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"
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
andallData_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
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
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