savetable: savetable

In mjhelf/Metaboseek: Metaboseek platform

savetable

Description

Save a peakTable from an xcms::XCMSnExp, xcms::xcmsSet or xcms::xsAnnotate object, and also keep track of analysis status via internal calls to writeStatus().

Usage

savetable(
  xset,
  importResultsFrom = NULL,
  filename = "tableoutxx",
  bparams = SerialParam(),
  intensities = list(ppm = 5, rtw = 5, rtrange = TRUE, areaMode = FALSE),
  rawdata = NULL,
  saveR = T,
  postProc = NULL
)

Arguments

xset	an xcms::XCMSnExp, xcms::xcmsSet or xcms::xsAnnotate object from which to extract the peaklist
importResultsFrom	if an MseekFT object is supplied here, will import Mseek intensities and other post-processing results if appropriate (same feature definitions, same files, same intensities)
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 Mseek 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, areaMode: if TRUE, get peak areas instead of mean intensities Not performed if intensities = NULL.
rawdata	named list of xcmsRaw objects (as returned by Mseek::loadRawM), required for Mseek EIC intensity extraction which is not performed if NULL.
saveR	save the xset object as .Rds file
postProc	list of SOME arguments passed to analyzeTable() for post processing, or NULL to skip processing. TODO: transisiton to do.call solution for postProc and document

Value

Returns a writeStatus object, writes to status.csv file as well as other .csv files (with processed or unprocessed peakTables) in current working directory.

mjhelf/Metaboseek documentation built on April 23, 2022, 12:09 p.m.