flagme: Analysis of Metabolomics GC/MS Data

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Fragment-level analysis of gas chromatography - mass spectrometry metabolomics data

Author
Mark Robinson <mark.robinson@imls.uzh.ch>, Riccardo Romoli <riccardo.romoli@unifi.it>
Date of publication
None
Maintainer
Mark Robinson <mark.robinson@imls.uzh.ch>, Riccardo Romoli <riccardo.romoli@unifi.it>
License
LGPL (>= 2)
Version
1.30.0

View on Bioconductor

Man pages

addAMDISPeaks
Add AMDIS peak detection results
addChromaTOFPeaks
Add ChromaTOF peak detection results
addXCMSPeaks
Add xcms/CAMERA peak detection results
betweenAlignment
Data Structure for "between" alignment of many GCMS samples
calcTimeDiffs
Calculate retention time shifts from profile alignments
clusterAlignment
Data Structure for a collection of all pairwise alignments of...
compress
Compress an alignment object
correlationAlignment
Function for correlation-based alignment strategy of multiple...
correlationAlignment-class
'"correlationAlignment-class"'
dp
Dynamic programming algorithm, given a similarity matrix
eitherMatrix
The 'eitherMatrix' class
exportSpectra
exportSpectra
gatherInfo
Gathers abundance informations from an alignment
imputePeaks
Imputatin of locations of peaks that were undetected
multipleAlignment
Data Structure for multiple alignment of many GCMS samples
normDotProduct
Normalized Dot Product
parseChromaTOF
Parser for ChromaTOF files
parseELU
Parser for ELU files
peaksAlignment
Data Structure for pairwise alignment of 2 GCMS samples
peaksDataset
Data Structure for raw GCMS data and peak detection results
plot
Plotting functions for GCMS data objects
plotImage
Plot of images of GCMS data
plotSpectra
plotSpectra
progressiveAlignment
Data Structure for progressive alignment of many GCMS samples
retFatMatrix
retFatMatrix
rmaFitUnit
Fits a robust linear model (RLM) for one metabolite

Files in this package

flagme/DESCRIPTION
flagme/NAMESPACE
flagme/R
flagme/R/0classes.R
flagme/R/addXCMSPeaks.R
flagme/R/betweenAlignment.R
flagme/R/clusterAlignment.R
flagme/R/correlationAlignment.R
flagme/R/dp.R
flagme/R/exportSpectra.R
flagme/R/gatherInfo.R
flagme/R/init.R
flagme/R/metrics.R
flagme/R/multipleAlignment.R
flagme/R/parse.R
flagme/R/peaksAlignment.R
flagme/R/peaksDataset.R
flagme/R/plotFragments.R
flagme/R/plotSpectra.R
flagme/R/progressiveAlignment.R
flagme/R/retFatMatrix.R
flagme/R/rmaFitUnit.R
flagme/build
flagme/build/vignette.rds
flagme/inst
flagme/inst/NEWS
flagme/inst/doc
flagme/inst/doc/flagme.R
flagme/inst/doc/flagme.Rnw
flagme/inst/doc/flagme.pdf
flagme/man
flagme/man/addAMDISPeaks.Rd
flagme/man/addChromaTOFPeaks.Rd
flagme/man/addXCMSPeaks.Rd
flagme/man/betweenAlignment.Rd
flagme/man/calcTimeDiffs.Rd
flagme/man/clusterAlignment.Rd
flagme/man/compress.Rd
flagme/man/correlationAlignment-class.Rd
flagme/man/correlationAlignment.Rd
flagme/man/dp.Rd
flagme/man/eitherMatrix.Rd
flagme/man/exportSpectra.Rd
flagme/man/gatherInfo.Rd
flagme/man/imputePeaks.Rd
flagme/man/multipleAlignment.Rd
flagme/man/normDotProduct.Rd
flagme/man/parseChromaTOF.Rd
flagme/man/parseELU.Rd
flagme/man/peaksAlignment.Rd
flagme/man/peaksDataset.Rd
flagme/man/plot.Rd
flagme/man/plotImage.Rd
flagme/man/plotSpectra.Rd
flagme/man/progressiveAlignment.Rd
flagme/man/retFatMatrix.Rd
flagme/man/rmaFitUnit.Rd
flagme/src
flagme/src/dp.c
flagme/src/flagme.h
flagme/src/init.c
flagme/src/pearson.c
flagme/vignettes
flagme/vignettes/flagme.Rnw
flagme/vignettes/readme.txt