flagme (version 1.28.0)

betweenAlignment: Data Structure for "between" alignment of many GCMS samples

Description

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

Usage

betweenAlignment(pD,cAList,pAList,impList,filterMin=3,gap=0.7,D=10,usePeaks=TRUE,df=30,verbose=TRUE)

Arguments

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

Value

betweenAlignment object

Details

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.

References

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

See Also

multipleAlignment

Examples

require(gcspikelite)
# see 'multipleAlignment'