betweenAlignment {flagme}R Documentation

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

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.

Value

betweenAlignment object

Author(s)

Mark Robinson

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'

[Package flagme version 1.0.0 Index]