processData: doxcms

In jaspershen/MetFlow: 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, mzdiff = -0.001,
  noise = 500, threads = 4, output.tic = TRUE, output.bpc = TRUE,
  output.rt.correction.plot = TRUE, min.fraction = 0.8,
  fill.peaks = FALSE)

Arguments

path	Work directory.
polarity	The polarity of data, "positive"or "negative".
ppm	see xcms.
peakwidth	See xcms.
snthresh	See xcms.
mzdiff	See xcms.
noise	See xcms.
threads	Number of threads.
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.

Value

Peak table.

Author(s)

Xiaotao Shen [e-mail]

jaspershen/MetFlow documentation built on Aug. 1, 2019, 4:36 p.m.