process_data

Raw MS data processing using xcms.

process_data(
  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,
  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.

group_for_figure

Which group you want to use to output TIC and BPC and EIC. Default is QC.

Value

Peak table.

Author

Xiaotao Shen shenxt1990@outlook.com