clusterAlignment {flagme} | R Documentation |
Store the raw data and optionally, information regarding signal peaks for a number of GCMS runs
clusterAlignment(pD,runs=1:length(pD@rawdata),timedf=NULL,usePeaks=TRUE,verbose=TRUE,...)
pD |
a peaksDataset object. |
runs |
vector of integers giving the samples to calculate set of pairwise alignments over. |
timedf |
list (length = the number of pairwise alignments) of matrices giving the expected time differences expected at each pair of peaks (used with usePeaks =TRUE , passed to peaksAlignment |
usePeaks |
logical, TRUE uses peakdata list, FALSE uses rawdata list for computing similarity. |
verbose |
logical, whether to print out info. |
... |
other arguments passed to peaksAlignment |
clusterAlignment computes the set of pairwise alignments.
clusterAlignment
object
Mark Robinson
Mark D Robinson (2008). Methods for the analysis of gas chromatography - mass spectrometry data PhD dissertation University of Melbourne.
require(gcspikelite) # paths and files gcmsPath<-paste(.find.package("gcspikelite"),"data",sep="/") cdfFiles<-dir(gcmsPath,"CDF",full=TRUE) eluFiles<-dir(gcmsPath,"ELU",full=TRUE) # read data, peak detection results pd<-peaksDataset(cdfFiles[1:2],mz=seq(50,550),rtrange=c(7.5,8.5)) pd<-addAMDISPeaks(pd,eluFiles[1:2]) ca<-clusterAlignment(pd, gap = .5,D=.05,df=30)