Analysis of Metabolomics GC/MS Data

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Documentation for package ‘flagme’ version 1.8.0

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.plotcA Plotting functions for GCMS data objects
.plotpA Plotting functions for GCMS data objects
.plotpD Plotting functions for GCMS data objects
addAMDISPeaks Add AMDIS peak detection results
addChromaTOFPeaks Add ChromaTOF peak detection results
betweenAlignment Data Structure for "between" alignment of many GCMS samples
betweenAlignment-class Data Structure for "between" alignment of many GCMS samples
betweenAlignment-show 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 GCMS runs
clusterAlignment-class Data Structure for a collection of all pairwise alignments of GCMS runs
clusterAlignment-plot Data Structure for a collection of all pairwise alignments of GCMS runs
clusterAlignment-show Data Structure for a collection of all pairwise alignments of GCMS runs
compress Compress an alignment object
compress-method Compress an alignment object
decompress Compress an alignment object
decompress-method Compress an alignment object
dp Dynamic programming algorithm, given a similarity matrix
eitherMatrix-class The 'eitherMatrix' class
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
multipleAlignment-class Data Structure for multiple alignment of many GCMS samples
multipleAlignment-show 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
peaksAlignment-class Data Structure for pairwise alignment of 2 GCMS samples
peaksAlignment-plot Data Structure for pairwise alignment of 2 GCMS samples
peaksAlignment-show Data Structure for pairwise alignment of 2 GCMS samples
peaksDataset Data Structure for raw GCMS data and peak detection results
peaksDataset-class Data Structure for raw GCMS data and peak detection results
peaksDataset-plot Data Structure for raw GCMS data and peak detection results
peaksDataset-show Data Structure for raw GCMS data and peak detection results
plot Plotting functions for GCMS data objects
plot-method Data Structure for a collection of all pairwise alignments of GCMS runs
plot-method Data Structure for pairwise alignment of 2 GCMS samples
plot-method Data Structure for raw GCMS data and peak detection results
plotImage Plot of images of GCMS data
plotImage-method Plot of images of GCMS data
progressiveAlignment Data Structure for progressive alignment of many GCMS samples
progressiveAlignment-class Data Structure for progressive alignment of many GCMS samples
progressiveAlignment-show Data Structure for progressive alignment of many GCMS samples
rmaFitUnit Fits a robust linear model (RLM) for one metabolite
show-method Data Structure for "between" alignment of many GCMS samples
show-method Data Structure for a collection of all pairwise alignments of GCMS runs
show-method Data Structure for multiple alignment of many GCMS samples
show-method Data Structure for pairwise alignment of 2 GCMS samples
show-method Data Structure for raw GCMS data and peak detection results
show-method Data Structure for progressive alignment of many GCMS samples