CAMERA (version 1.28.0)

getIsotopeCluster: Retrieve the annotatad isotopes

Description

Extract all annotated isotope cluster. Returns a list with one element per cluster. A element contains the charge of the molecule and a peakmatrix with mz and intensity value.

Usage

getIsotopeCluster(object, number=NULL, value="maxo", sampleIndex=NULL)

Arguments

object

xsAnnotate object

number

Set to NULL extract all isotope cluster or to specific chosen ones

value

Which intensity values should be extracted. Allowed values are: maxo, into, intb

sampleIndex

Selection vector with indexes to select from which sample(s) the intensity values should be retrieved. If set to NULL the sample is selected, which has been chosen for the pseudospectra in the grouping step

Details

This method extract the isotope annotation from a xsAnnotate object. The order of the resulting list is the same as the one in the peaklist, see getPeaklist.

Examples

  #single sample
  library(CAMERA)
  file <- system.file('mzdata/MM14.mzdata', package = "CAMERA")
  xs   <- xcmsSet(file, method="centWave", ppm=30, peakwidth=c(5,10))
  an   <- xsAnnotate(xs)
  an   <- groupFWHM(an)
  an   <- findIsotopes(an) 
  isolist <- getIsotopeCluster(an)
  isolist[[10]] #get IsotopeCluster 10

  #multiple sample
  library(faahKO)
  xs <- group(faahko)
  xs <- fillPeaks(xs)
  an   <- xsAnnotate(xs)
  an   <- groupFWHM(an)
  an   <- findIsotopes(an) 
  isolist <- getIsotopeCluster(an)

  #Select from multiple samples
  
  isolist <- getIsotopeCluster(an, sampleIndex=c(1,2,5))
  
  ##Interaction with Rdisop
 ## Not run: 
#   library(Rdisop)
#   isotopes.decomposed <- lapply(isolist,function(x) {
#     decomposeIsotopes(x$peaks[,1],x$peaks[,2],z=x$charge);
#   }) #decomposed isotope cluster, filter steps are recommended
#  ## End(Not run)