diff --git a/DESCRIPTION b/DESCRIPTION index 80956294..811e90ab 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -158,4 +158,5 @@ Collate: 'writemzdata.R' 'writemztab.R' 'xcmsSource.R' - 'zzz.R' \ No newline at end of file + 'zzz.R' + diff --git a/R/XcmsExperiment.R b/R/XcmsExperiment.R index 6a222aec..c695da70 100644 --- a/R/XcmsExperiment.R +++ b/R/XcmsExperiment.R @@ -1232,7 +1232,7 @@ setMethod( function(object, method = c("all", "closest_rt", "closest_mz", "largest_tic", "largest_bpi"), msLevel = 2L, expandRt = 0, expandMz = 0, ppm = 0, - skipFilled = FALSE, peaks = character(), peaksInfo = c("rt", "mz") + skipFilled = FALSE, peaks = character(), peaksInfo = c("rt", "mz"), return.type = c("Spectra", "List"), BPPARAM = bpparam()) { if (hasAdjustedRtime(object)) object <- applyAdjustedRtime(object) diff --git a/man/XcmsExperiment.Rd b/man/XcmsExperiment.Rd index 9bfc0437..28516110 100644 --- a/man/XcmsExperiment.Rd +++ b/man/XcmsExperiment.Rd @@ -396,6 +396,10 @@ also parameter \code{type} below for additional information.} \item{keepFeatures}{for most subsetting functions (\code{[}, \code{filterFile}): \code{logical(1)}: wheter eventually present feature definitions should be retained in the returned (filtered) object.} + +\item{peaksInfo}{For \code{chromPeakSpectra}: \code{character} vector of additional +information from \code{chromPeaks()} to be added to the spectra object. The +columns names will be appended with "peaks_".} } \description{ The \code{XcmsExperiment} is a data container for \code{xcms} preprocessing results diff --git a/man/chromPeakSpectra.Rd b/man/chromPeakSpectra.Rd index 40fef183..8cd9439a 100644 --- a/man/chromPeakSpectra.Rd +++ b/man/chromPeakSpectra.Rd @@ -18,6 +18,7 @@ chromPeakSpectra(object, ...) ppm = 0, skipFilled = FALSE, peaks = character(), + peaksInfo = c("rt", "mz"), return.type = c("Spectra", "List"), BPPARAM = bpparam() )