processData: processData

In jaspershen/metflow2: Comprehensitive tools for metabolomics data processing and data analysis

Description

Raw MS data processing using xcms.

Usage

processData(
  path = ".",
  polarity = c("positive", "negative"),
  ppm = 15,
  peakwidth = c(5, 30),
  snthresh = 10,
  prefilter = c(3, 500),
  fitgauss = FALSE,
  integrate = 2,
  mzdiff = 0.01,
  noise = 500,
  threads = 6,
  binSize = 0.025,
  bw = 5,
  output.tic = TRUE,
  output.bpc = TRUE,
  output.rt.correction.plot = TRUE,
  min.fraction = 0.5,
  fill.peaks = FALSE,
  output.peak.eic = TRUE,
  is.table = "is.table.xlsx",
  is.mz.tolerance = 25,
  is.rt.tolerance = 50,
  group.for.figure = "QC"
)

Arguments

path	Work directory.
polarity	The polarity of data, "positive"or "negative".
ppm	see xcms.
peakwidth	See xcms.
snthresh	See xcms.
prefilter	See xcms.
fitgauss	see xcms.
integrate	see xcms.
mzdiff	see xcms.
noise	See xcms.
threads	Number of threads.
binSize	see xcms.
bw	see xcms.
output.tic	Output TIC plot or not.
output.bpc	Output BPC plot or not.
output.rt.correction.plot	Output rt correction plot or not.
min.fraction	See xcms.
fill.peaks	Fill peaks NA or not.
output.peak.eic	Output some peaks EIC or not. If you want to output this, please place the 'is.xlsx' in the folder. And three columns, name, mz and rt.
is.table	International standard table name.
is.mz.tolerance	mz tolerance for internal standards. Default is 25 ppm.
is.rt.tolerance	RT tolerance for internal standards. Default is 50 s..
group.for.figure	Which group you want to use to output TIC and BPC and EIC. Default is QC.

Value

Peak table.

Author(s)

Xiaotao Shen [e-mail]

jaspershen/metflow2 documentation built on Aug. 15, 2021, 4:38 p.m.