getdata2: Get XCMSnExp object in one step from structured folder path...

In enviGCMS: GC/LC-MS Data Analysis for Environmental Science

Get XCMSnExp object in one step from structured folder path for xcms 3.

Description

Get XCMSnExp object in one step from structured folder path for xcms 3.

Usage

getdata2(
  path,
  index = FALSE,
  snames = NULL,
  sclass = NULL,
  phenoData = NULL,
  BPPARAM = BiocParallel::SnowParam(),
  mode = "onDisk",
  ppp = xcms::CentWaveParam(ppm = 5, peakwidth = c(5, 25), prefilter = c(3, 5000)),
  rtp = xcms::ObiwarpParam(binSize = 1),
  gpp = xcms::PeakDensityParam(sampleGroups = 1, minFraction = 0.67, bw = 2, binSize =
    0.025),
  fpp = xcms::FillChromPeaksParam()
)

Arguments

path	the path to your data
index	the index of the files
snames	sample names. By default the file name without extension is used
sclass	sample classes.
phenoData	data.frame or NAnnotatedDataFrame defining the sample names and classes and other sample related properties. If not provided, the argument sclass or the subdirectories in which the samples are stored will be used to specify sample grouping.
BPPARAM	used for BiocParallel package
mode	'inMemory' or 'onDisk' see ‘?MSnbase::readMSData' for details, default ’onDisk'
ppp	parameters for peaks picking, e.g. xcms::CentWaveParam()
rtp	parameters for retention time correction, e.g. xcms::ObiwarpParam()
gpp	parameters for peaks grouping, e.g. xcms::PeakDensityParam()
fpp	parameters for peaks filling, e.g. xcms::FillChromPeaksParam(), PeakGroupsParam()

Details

This is a wrap function for metabolomics data process for xcms 3.

Value

a XCMSnExp object with processed data

See Also

getdata,getmzrt

enviGCMS documentation built on Feb. 16, 2023, 8:08 p.m.