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 |
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 |
logical, |
verbose |
logical, whether to print out info. |
... |
other arguments passed to |
clusterAlignment computes the set of pairwise alignments.
clusterAlignment
object
Mark Robinson, Riccardo Romoli
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=0.5, D=0.05, df=30, metric=1, type=1)