# Analysis of Metabolomics GC/MS Data

## Documentation for package ‘flagme’ version 1.34.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

.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
addXCMSPeaks | Add xcms/CAMERA 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
corPrt | Retention Time Penalized Correlation
decompress | Compress an alignment object
decompress-method | Compress an alignment object
dp | Dynamic programming algorithm, given a similarity matrix
dynRT | dynRT
eitherMatrix-class | 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
multipleAlignment-class | Data Structure for multiple alignment of many GCMS samples
multipleAlignment-show | Data Structure for multiple alignment of many GCMS samples
ndpRT | Retention Time Penalized Normalized Dot Product
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
plotMultipleSpectra | plotMultipleSpectra
plotSpectra | plotSpectra
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
retFatMatrix | retFatMatrix
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