Entry: addAMDISPeaks
Aliases: addAMDISPeaks
Keywords: manip
Description: Add AMDIS peak detection results
URL: ../../../library/flagme/html/addAMDISPeaks.html

Entry: addChromaTOFPeaks
Aliases: addChromaTOFPeaks
Keywords: manip
Description: Add ChromaTOF peak detection results
URL: ../../../library/flagme/html/addChromaTOFPeaks.html

Entry: betweenAlignment
Aliases: betweenAlignment betweenAlignment-class betweenAlignment-show show,betweenAlignment-method
Keywords: classes
Description: Data Structure for "between" alignment of many GCMS samples
URL: ../../../library/flagme/html/betweenAlignment.html

Entry: calcTimeDiffs
Aliases: calcTimeDiffs
Keywords: manip
Description: Calculate retention time shifts from profile alignments
URL: ../../../library/flagme/html/calcTimeDiffs.html

Entry: clusterAlignment
Aliases: clusterAlignment clusterAlignment-show clusterAlignment-class clusterAlignment-plot show,clusterAlignment-method plot,clusterAlignment-method
Keywords: classes
Description: Data Structure for a collection of all pairwise alignments of GCMS runs
URL: ../../../library/flagme/html/clusterAlignment.html

Entry: compress
Aliases: compress decompress compress,clusterAlignment-method decompress,clusterAlignment-method compress,peaksAlignment-method decompress,peaksAlignment-method compress,progressiveAlignment-method decompress,progressiveAlignment-method
Keywords: manip
Description: Compress an alignment object
URL: ../../../library/flagme/html/compress.html

Entry: dp
Aliases: dp
Keywords: manip
Description: Dynamic programming algorithm, given a similarity matrix
URL: ../../../library/flagme/html/dp.html

Entry: gatherInfo
Aliases: gatherInfo
Keywords: manip
Description: Gathers abundance informations from an alignment
URL: ../../../library/flagme/html/gatherInfo.html

Entry: imputePeaks
Aliases: imputePeaks
Keywords: manip
Description: Imputatin of locations of peaks that were undetected
URL: ../../../library/flagme/html/imputePeaks.html

Entry: multipleAlignment-class
Aliases: multipleAlignment-class multipleAlignment-show multipleAlignment show,multipleAlignment-method
Keywords: classes
Description: Data Structure for multiple alignment of many GCMS samples
URL: ../../../library/flagme/html/multipleAlignment.html

Entry: normDotProduct
Aliases: normDotProduct
Keywords: manip
Description: Normalized Dot Product
URL: ../../../library/flagme/html/normDotProduct.html

Entry: parseChromaTOF
Aliases: parseChromaTOF
Keywords: manip
Description: Parser for ChromaTOF files
URL: ../../../library/flagme/html/parseChromaTOF.html

Entry: parseELU
Aliases: parseELU
Keywords: manip
Description: Parser for ELU files
URL: ../../../library/flagme/html/parseELU.html

Entry: peaksAlignment-class
Aliases: peaksAlignment-class peaksAlignment-show peaksAlignment-plot peaksAlignment show,peaksAlignment-method plot,peaksAlignment-method
Keywords: classes
Description: Data Structure for pairwise alignment of 2 GCMS samples
URL: ../../../library/flagme/html/peaksAlignment.html

Entry: peaksDataset
Aliases: peaksDataset-class peaksDataset-show peaksDataset-plot peaksDataset show,peaksDataset-method plot,peaksDataset-method
Keywords: classes
Description: Data Structure for raw GCMS data and peak detection results
URL: ../../../library/flagme/html/peaksDataset.html

Entry: plot.peaksDataset
Aliases: plot .plotpA .plotpD .plotcA
Keywords: classes
Description: Plotting functions for GCMS data objects
URL: ../../../library/flagme/html/plot.html

Entry: plotImage
Aliases: plotImage plotImage,peaksDataset-method
Keywords: classes
Description: Plot of images of GCMS data
URL: ../../../library/flagme/html/plotImage.html

Entry: progressiveAlignment-class
Aliases: progressiveAlignment-class progressiveAlignment-show progressiveAlignment show,progressiveAlignment-method
Keywords: classes
Description: Data Structure for progressive alignment of many GCMS samples
URL: ../../../library/flagme/html/progressiveAlignment.html

Entry: rmaFitUnit
Aliases: rmaFitUnit
Keywords: manip
Description: Fits a robust linear model (RLM) for one metabolite
URL: ../../../library/flagme/html/rmaFitUnit.html
