compress {flagme} | R Documentation |
Many of the peaks are not similar. So, the set of pairwise similarity matrices can be compressed.
compress(object,verbose=TRUE,...) decompress(object,verbose=TRUE,...)
object |
a |
verbose |
logical, whether to print out information |
... |
further arguments |
Using sparse matrix representations, a significant compression can be achieved. Here, we use the matrix.csc
class of the SpareM
package.
an object of the same type as the input object
Mark Robinson
Mark D Robinson (2008). Methods for the analysis of gas chromatography - mass spectrometry data PhD dissertation University of Melbourne.
peaksAlignment
, clusterAlignment
, progressiveAlignment
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]) # pairwise alignment (it is compressed by default) ca<-clusterAlignment(pd, usePeaks = TRUE, df = 20, metric=1, type=1) object.size(ca) # decompress ca<-decompress(ca) object.size(ca)