Added expansion factors for the mz and rt range used in fillPeaks.chrom.

R/MPI.R

@@ -333,6 +333,10 @@ fillPeaksChromPar <- function(arg) {
   prof <- params$prof
   rtcor <- params$rtcor
   peakrange <- params$peakrange
+  expand.mz <- params$expand.mz
+  expand.rt <- params$expand.rt
+  min.width.mz <- params$min.width.mz
+  min.width.rt <- params$min.width.rt
   gvals <- params$gvals$gvals
 
   lcraw <- xcmsRaw(arg$file, profmethod=params$prof$method, profstep = 0)
@@ -358,6 +362,31 @@ fillPeaksChromPar <- function(arg) {
       warning("(corrected) retention time vector length mismatch for ", basename(arg$file))
     }
 
+
+  # Expanding the peakrange
+  peakrange[,"mzmax"]  <-  peakrange[,"mzmax"]   +    (   (peakrange[,"mzmax"]-peakrange[,"mzmin"])/2    )*(expand.mz-1)
+  peakrange[,"mzmin"]  <-  peakrange[,"mzmin"]   -    (   (peakrange[,"mzmax"]-peakrange[,"mzmin"])/2    )*(expand.mz-1)
+  peakrange[,"rtmax"]  <-  peakrange[,"rtmax"]   +    (   (peakrange[,"rtmax"]-peakrange[,"rtmin"])/2    )*(expand.rt-1)
+  peakrange[,"rtmin"]  <-  peakrange[,"rtmin"]   -    (   (peakrange[,"rtmax"]-peakrange[,"rtmin"])/2    )*(expand.rt-1)
+
+
+  # Setting a minimum peakwidth for mz and rt range
+  idx.expand.mz = (peakrange[,"mzmax"] - peakrange[,"mzmin"]) < min.width.mz
+  peakrange[idx.expand.mz,"mzmin"]   =  rowMeans(    peakrange[ idx.expand.mz , c("mzmin","mzmax") ,drop=F]    )   -min.width.mz/2
+  peakrange[idx.expand.mz,"mzmax"]   =  rowMeans(    peakrange[ idx.expand.mz , c("mzmin","mzmax") ,drop=F]    )   +min.width.mz/2
+
+  idx.expand.rt = (peakrange[,"rtmax"] - peakrange[,"rtmin"]) < min.width.rt
+  peakrange[idx.expand.rt,"rtmin"]   =  rowMeans(    peakrange[ idx.expand.rt , c("rtmin","rtmax") ,drop=F]    )   -min.width.rt/2
+  peakrange[idx.expand.rt,"rtmax"]   =  rowMeans(    peakrange[ idx.expand.rt , c("rtmin","rtmax") ,drop=F]    )   +min.width.rt/2
+
+
+  # Making sure the expanded peakrange doesn't exceed the RT range in the file
+  peakrange[        peakrange[,"rtmin"]<min(lcraw@scantime)            ,"rtmin"]     <-     min(lcraw@scantime)
+  peakrange[        peakrange[,"rtmax"]>max(lcraw@scantime)            ,"rtmax"]     <-     max(lcraw@scantime)
+
+
+
+
     naidx <- which(is.na(gvals[,myID]))
 
     newpeaks <- getPeaks(lcraw, peakrange[naidx,,drop=FALSE], step = prof$step)

R/xcmsSet.R

@@ -1368,7 +1368,7 @@ setMethod("plotrt", "xcmsSet", function(object, col = NULL, ty = NULL, leg = TRU
 
 setGeneric("fillPeaks.chrom", function(object, ...) standardGeneric("fillPeaks.chrom"))
 
-setMethod("fillPeaks.chrom", "xcmsSet", function(object, nSlaves=NULL) {
+setMethod("fillPeaks.chrom", "xcmsSet", function(object, nSlaves=NULL,expand.mz=1,expand.rt=1,min.width.mz=0,min.width.rt=0) {
   ## development mockup:
   if (FALSE) {
     library(xcms)
@@ -1440,7 +1440,11 @@ assign("gvals", gvals, envir = gvals_env)
                dataCorrection=object@dataCorrection,
                polarity=object@polarity,
                rtcor=object@rt$corrected[[as.numeric(x["id"])]],
-               peakrange=peakrange))
+               peakrange=peakrange,
+               expand.mz=expand.mz,
+               expand.rt=expand.rt,
+               min.width.mz=min.width.mz,
+               min.width.rt=min.width.rt))
       }
     })
 

man/fillPeaks.chrom-methods.Rd

@@ -12,14 +12,18 @@
 \section{Methods}{
 \describe{
 \item{object = "xcmsSet"}{
-  \code{fillPeaks.chrom(object, nSlaves=0)}
+  \code{fillPeaks.chrom(object, nSlaves=0,expand.mz=1,expand.rt=1,min.width.mz=0,min.width.rt=0)}
 }
 }}
 
 \arguments{
   \item{object}{the \code{xcmsSet} object}
   \item{nSlaves}{number of slaves/cores to be used for parallel peak filling.
     MPI is used if installed, otherwise the snow package is employed for multicore support.}
+  \item{expand.mz}{Expansion factor for the m/z range used for integration.}
+  \item{expand.rt}{Expansion factor for the retention time range used for integration.}
+  \item{min.width.mz}{Minimum m/z range used for integration.}
+  \item{min.width.rt}{Minimum retention time range used for integration.}
 }
 \details{
   After peak grouping, there will always be peak groups that do not

man/getPeaks-methods.Rd

@@ -15,7 +15,7 @@
 }
 }}
 \arguments{
-  \item{object}{the \code{xcmsSet} object}
+  \item{object}{the \code{xcmsRaw} object}
   \item{peakrange}{
     matrix or data frame with 4 columns: \code{mzmin}, \code{mzmax},
     \code{rtmin}, \code{rtmax} (they must be in that order or named)