SIMAT: GC-SIM-MS data processing and alaysis tool

This package provides a pipeline for analysis of GC-MS data acquired in selected ion monitoring (SIM) mode. The tool also provides a guidance in choosing appropriate fragments for the targets of interest by using an optimization algorithm. This is done by considering overlapping peaks from a provided library by the user.

Author
Mo R. Nezami Ranjbar <nranjbar@vt.edu>
Date of publication
None
Maintainer
Mo R. Nezami Ranjbar <nranjbar@vt.edu>
License
GPL-2
Version
1.6.0
URLs

View on Bioconductor

Man pages

getEIC
Get the EIC of a peak
getPeak
Get all peaks corresponding to targets in several runs
getPeakScore
Calculate the similarity score for all peaks
getRI
Generate a calibration function
getRIStandard
Get the RI standard information
getScore
Calculate similarity score for a peak
getTarget
Get target information
getTargetTable
Get target table information
Library
Extracted compound information from an MSL library.
optFrag
Fragment selection through optimization
plotEIC
Plotting EIC of one peak
plotTIC
Plotting TIC of one run
putTargetTable
Put target table information
readCDF
Read raw mass spectrometry data in netCDF files
readMSL
Read mass spectral library (MSL) files
RItable
Extracted RI standard information from a 'csv' file.
Run
Extracted peaks from one SIM run.
SIMAT-package
This package is for processing GC-SIM-MS data
Targets
Targets information in a list.
target.table
Extracted target information from a 'csv' file.
writeMSL
Write targets information into a file with mass spectral...

Files in this package

SIMAT/DESCRIPTION
SIMAT/NAMESPACE
SIMAT/NEWS
SIMAT/R
SIMAT/R/getEIC.R
SIMAT/R/getPeak.R
SIMAT/R/getPeakScore.R
SIMAT/R/getRI.R
SIMAT/R/getRIStandard.R
SIMAT/R/getScore.R
SIMAT/R/getTarget.R
SIMAT/R/getTargetTable.R
SIMAT/R/optFrag.R
SIMAT/R/plotEIC.R
SIMAT/R/plotTIC.R
SIMAT/R/putTargetTable.R
SIMAT/R/readCDF.R
SIMAT/R/readMSL.R
SIMAT/R/writeMSL.R
SIMAT/SIMAT
SIMAT/build
SIMAT/build/vignette.rds
SIMAT/data
SIMAT/data/Library.rda
SIMAT/data/RItable.rda
SIMAT/data/Run.rda
SIMAT/data/Targets.rda
SIMAT/data/target.table.rda
SIMAT/inst
SIMAT/inst/doc
SIMAT/inst/doc/SIMAT-vignette.R
SIMAT/inst/doc/SIMAT-vignette.Rnw
SIMAT/inst/doc/SIMAT-vignette.pdf
SIMAT/inst/extdata
SIMAT/inst/extdata/1_QC.CDF
SIMAT/inst/extdata/RIStandards.csv
SIMAT/inst/extdata/TargetTable.txt
SIMAT/inst/extdata/Targets_1.MSL
SIMAT/inst/unitTests
SIMAT/inst/unitTests/test_getEIC.R
SIMAT/inst/unitTests/test_getPeak.R
SIMAT/inst/unitTests/test_getPeakScore.R
SIMAT/inst/unitTests/test_getRI.R
SIMAT/inst/unitTests/test_getRIStandard.R
SIMAT/inst/unitTests/test_getScore.R
SIMAT/inst/unitTests/test_getTarget.R
SIMAT/inst/unitTests/test_getTargetTable.R
SIMAT/inst/unitTests/test_optFrag.R
SIMAT/inst/unitTests/test_plotEIC.R
SIMAT/inst/unitTests/test_plotTIC.R
SIMAT/inst/unitTests/test_putTargetTable.R
SIMAT/inst/unitTests/test_readCDF.R
SIMAT/inst/unitTests/test_readMSL.R
SIMAT/inst/unitTests/test_writeMSL.R
SIMAT/man
SIMAT/man/Library.Rd
SIMAT/man/RItable.Rd
SIMAT/man/Run.Rd
SIMAT/man/SIMAT-package.Rd
SIMAT/man/Targets.Rd
SIMAT/man/getEIC.Rd
SIMAT/man/getPeak.Rd
SIMAT/man/getPeakScore.Rd
SIMAT/man/getRI.Rd
SIMAT/man/getRIStandard.Rd
SIMAT/man/getScore.Rd
SIMAT/man/getTarget.Rd
SIMAT/man/getTargetTable.Rd
SIMAT/man/optFrag.Rd
SIMAT/man/plotEIC.Rd
SIMAT/man/plotTIC.Rd
SIMAT/man/putTargetTable.Rd
SIMAT/man/readCDF.Rd
SIMAT/man/readMSL.Rd
SIMAT/man/target.table.Rd
SIMAT/man/writeMSL.Rd
SIMAT/tests
SIMAT/tests/runTests.R
SIMAT/vignettes
SIMAT/vignettes/SIMAT-vignette.Rnw
SIMAT/vignettes/dsPeaks.rds