SIMAT: GC-SIM-MS data processing and alaysis tool
Version 1.8.0

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.

AuthorMo R. Nezami Ranjbar <nranjbar@vt.edu>
Bioconductor views MassSpectrometry Metabolomics Software
Date of publicationNone
MaintainerMo R. Nezami Ranjbar <nranjbar@vt.edu>
LicenseGPL-2
Version1.8.0
URL http://omics.georgetown.edu/SIMAT.html
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SIMAT")

Getting started

Package overview

Popular man pages

getPeakScore: Calculate the similarity score for all peaks
getRIStandard: Get the RI standard information
getScore: Calculate similarity score for a peak
getTarget: Get target information
plotEIC: Plotting EIC of one peak
plotTIC: Plotting TIC of one run
readMSL: Read mass spectral library (MSL) files
See all...

All man pages Function index File listing

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...

Functions

Library Man page
RItable Man page
Run Man page
SIMAT Man page
SIMAT-package Man page
Targets Man page
getEIC Man page Source code
getPeak Man page Source code
getPeakScore Man page Source code
getRI Man page Source code
getRIStandard Man page Source code
getScore Man page Source code
getTarget Man page Source code
getTargetTable Man page Source code
optFrag Man page Source code
plotEIC Man page Source code
plotTIC Man page Source code
putTargetTable Man page Source code
readCDF Man page Source code
readMSL Man page Source code
target.table Man page
writeMSL Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/getEIC.R
R/getPeak.R
R/getPeakScore.R
R/getRI.R
R/getRIStandard.R
R/getScore.R
R/getTarget.R
R/getTargetTable.R
R/optFrag.R
R/plotEIC.R
R/plotTIC.R
R/putTargetTable.R
R/readCDF.R
R/readMSL.R
R/writeMSL.R
SIMAT
build
build/vignette.rds
data
data/Library.rda
data/RItable.rda
data/Run.rda
data/Targets.rda
data/target.table.rda
inst
inst/doc
inst/doc/SIMAT-vignette.R
inst/doc/SIMAT-vignette.Rnw
inst/doc/SIMAT-vignette.pdf
inst/extdata
inst/extdata/1_QC.CDF
inst/extdata/RIStandards.csv
inst/extdata/TargetTable.txt
inst/extdata/Targets_1.MSL
inst/unitTests
inst/unitTests/test_getEIC.R
inst/unitTests/test_getPeak.R
inst/unitTests/test_getPeakScore.R
inst/unitTests/test_getRI.R
inst/unitTests/test_getRIStandard.R
inst/unitTests/test_getScore.R
inst/unitTests/test_getTarget.R
inst/unitTests/test_getTargetTable.R
inst/unitTests/test_optFrag.R
inst/unitTests/test_plotEIC.R
inst/unitTests/test_plotTIC.R
inst/unitTests/test_putTargetTable.R
inst/unitTests/test_readCDF.R
inst/unitTests/test_readMSL.R
inst/unitTests/test_writeMSL.R
man
man/Library.Rd
man/RItable.Rd
man/Run.Rd
man/SIMAT-package.Rd
man/Targets.Rd
man/getEIC.Rd
man/getPeak.Rd
man/getPeakScore.Rd
man/getRI.Rd
man/getRIStandard.Rd
man/getScore.Rd
man/getTarget.Rd
man/getTargetTable.Rd
man/optFrag.Rd
man/plotEIC.Rd
man/plotTIC.Rd
man/putTargetTable.Rd
man/readCDF.Rd
man/readMSL.Rd
man/target.table.Rd
man/writeMSL.Rd
tests
tests/runTests.R
vignettes
vignettes/SIMAT-vignette.Rnw
vignettes/dsPeaks.rds
SIMAT documentation built on May 20, 2017, 10:42 p.m.

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