group.nearest {xcms} | R Documentation |
Group peaks together across samples by creating a master peak list and assigning corresponding peaks from all samples. It is inspired by the alignment algorithm of mzMine. For further details check http://mzmine.sourceforge.net/ and
Katajamaa M, Miettinen J, Oresic M: MZmine: Toolbox for processing and visualization of mass spectrometry based molecular profile data. Bioinformatics (Oxford, England) 2006, 22:634?636.
Currently, there is no equivalent to minfrac
or minsamp
.
object |
the |
mzVsRTbalance |
Multiplicator for mz value before calculating the (euclidean) distance between two peaks. |
mzCheck |
Maximum tolerated distance for mz. |
rtCheck |
Maximum tolerated distance for RT. |
kNN |
Number of nearest Neighbours to check |
An xcmsSet
object with peak group assignments and statistics.
group(object, mzVsRTbalance=10, mzCheck=0.2, rtCheck=15, kNN=10)
xcmsSet-class
,
group.density
and
group.mzClust
## Not run: library(xcms) library(faahKO) ## These files do not have this problem to correct for but just for an example cdfpath <- system.file("cdf", package = "faahKO") cdffiles <- list.files(cdfpath, recursive = TRUE, full.names = TRUE) xset<-xcmsSet(cdffiles) gxset<-group(xset, method="nearest") ## this is the same as # gxset<-group.nearest(xset) nrow(gxset@groups) == 1096 ## the number of features before minFrac post.minFrac<-function(object, minFrac=0.5){ ix.minFrac<-sapply(1:length(unique(sampclass(object))), function(x, object, mf){ meta<-groups(object) minFrac.idx<-numeric(length=nrow(meta)) idx<-which(meta[,levels(sampclass(object))[x]] >= mf*length(which(levels(sampclass(object))[x] == sampclass(object)) )) minFrac.idx[idx]<-1 return(minFrac.idx) }, object, minFrac) ix.minFrac<-as.logical(apply(ix.minFrac, 1, sum)) ix<-which(ix.minFrac == TRUE) return(ix) } ## using the above function we can get a post processing minFrac idx<-post.minFrac(gxset) gxset.post<-gxset ## copy the xcmsSet object gxset.post@groupidx<-gxset@groupidx[idx] gxset.post@groups<-gxset@groups[idx,] nrow(gxset.post@groups) == 465 ## this is the number of features after minFrac ## End(Not run)