| .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 |