process_data: process_data

In tidymass/massprocesser: Comprehensitive tools for raw metabolomics data processing

process_data

Description

Raw MS data processing using xcms.

Usage

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",
  detect_peak_algorithm = c("xcms", "massprocesser")
)

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.
detect_peak_algorithm	Use the algorithm from xcms or local from massprocesser

Value

Peak table.

Author(s)

Xiaotao Shen [e-mail]

tidymass/massprocesser documentation built on May 7, 2023, 10:18 p.m.