enviGCMS (version 0.7.1)

getdata2: 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()
)

Value

a XCMSnExp object with processed data

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.

See Also

getdata,getmzrt