| savetable {Mosaic} | R Documentation |
Write or update a status dataframe with custom messages, time stamp and time elapsed since last status. Useful to document time consumed analysis by steps.
savetable(xset, status = NULL, fill = FillChromPeaksParam(expandMz = 0.005, expandRt = 5, ppm = 3), nonfill = F, filename = "tableoutxx.csv", bparams = SnowParam(workers = 1), intensities = list(ppm = 5, rtw = 5, rtrange = T), rawdata = NULL, saveR = T)
xset |
an xcms::XCMSnExp, xcms::xcmsSet or xcms::xsAnnotate object from which to extract the peaklist |
status |
a writeStatus object to be modified and returned by the function. |
fill |
xcms::FillChromPeaksParam object to specify how to fill peaks (only works if xset is an XCMSnExp object). No peak filling if NULL. |
nonfill |
also write the non-filled peaktable data? TRUE or FALSE |
filename |
filename to use when writing the csv file (including file extension). "_filled" will be added for filled data. |
bparams |
BBPARAMs (BiocParallel::BiocParallelParam object with parameters for parallel computing used in fill peaks) |
intensities |
list of parameters for Mosaic EIC intensity extraction (for each feature in the peaklist). ppm: mz window, rtw: rt window (+/- seconds), rtrange: if TRUE, rtw extends from rtmin and rtmax, if FALSE rtw centers around value in column rt. Not performed if intensities = NULL. |
rawdata |
named list of xcmsRaw objects (as returned by Mosaic::loadRawM), required for Mosaic EIC intensity extraction which is not performed if NULL. |
saveR |
save the xset object as .Rdata file |