betweenAlignment: Data Structure for "between" alignment of many GCMS samples
In flagme: Analysis of Metabolomics GC/MS Data

Description Usage Arguments Details Value Author(s) References See Also Examples

This function creates a "between" alignment (i.e. comparing merged peaks)

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betweenAlignment(pD, cAList, pAList, impList, filterMin = 1, gap = 0.7, 
	                    D = 10, usePeaks = TRUE, df = 30, verbose = TRUE, 
                        metric = 2,  type = 2, penality = 0.2)

`pD`	a `peaksDataset` object
`cAList`	`list` of `clusterAlignment` objects, one for each experimental group
`pAList`	`list` of `progressiveAlignment` objects, one for each experimental group
`impList`	`list` of imputation lists
`filterMin`	minimum number of peaks within a merged peak to be kept in the analysis
`gap`	gap parameter
`D`	retention time penalty parameter
`usePeaks`	logical, whether to use peaks (if `TRUE`) or the full 2D profile alignment (if `FALSE`)
`df`	distance from diagonal to calculate similarity
`verbose`	logical, whether to print information
`metric`	numeric, different algorithm to calculate the similarity matrix between two mass spectrum. `metric=1` call `normDotProduct()`; `metric=2` call `ndpRT()`; `metric=3` call `corPrt()`
`type`	numeric, two different type of alignment function
`penality`	penalization applied to the matching between two mass spectra if `(t1-t2)>D`

betweenAlignment objects gives the data structure which stores the result of an alignment across several "pseudo" datasets. These pseudo datasets are constructed by merging the "within" alignments.

betweenAlignment object

Mark Robinson

Mark D Robinson (2008). Methods for the analysis of gas chromatography - mass spectrometry data PhD dissertation University of Melbourne.

multipleAlignment