betweenAlignment {flagme} | R Documentation |
This function creates a "between" alignment (i.e. comparing merged peaks)
betweenAlignment(pD,cAList,pAList,impList,filterMin=3,gap=0.7,D=10,usePeaks=TRUE,df=30,verbose=TRUE)
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 |
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.
require(gcspikelite) # see 'multipleAlignment'