xcmsProcessingMS1

Import msDataFiles, filter ion_mode, find peaks using centWaveParam, correct RT, group peaks using peaksGroup, fill peaks by xcms at MS1 Level

Usage

xcmsProcessingMS1(
  xcms.xcms,
  ion_mode = NA,
  xcms_param = list(findChromPeaks = xcms::CentWaveParam(), groupChromPeaks =
    xcms::PeakDensityParam(sampleGroups = "A")),
  adjustRT = T,
  chromPeaks_fix_mz_ppm = NULL,
  chromPeaks_max_mz_ppm = NULL,
  beta_cor_thresh = NULL,
  BPPARAM = BiocParallel::SnowParam(workers = max(1L, floor(parallel::detectCores()/3)),
    progressbar = T),
  ...
)

Arguments

ion_mode

to filter ion_mode, 1: positive, 0: negative, import when scans with both pos and neg

beta_cor_thresh

optional numeric; if set, fill NA beta_cor after merge with chromPeakSummary() (finite CentWave scores are kept), then drop chromPeaks below this value (remaining NA scores are dropped). Default NULL skips fill and filtering.

msDataFiles

char ms file (full) paths

peaksGroup

vector to xcms::PeakGroupsParam(sampleGroups), should contain "QC"

centWaveParam

xcms::CentWaveParam()

Value

xcms