metaboProc: Metabolomics files process

In jordirofes/OmniOmics: Analysis of metabolomics (LC-MS) and transcriptomics (Microarray) data

Metabolomics files process

Description

Processes a OnDiskMSnExp/MSnExp object with XCMS and annotates it with CAMERA or CliqueMS.

Usage

metaboProc(
  object,
  polarity = "positive",
  groupvar,
  peakwidth,
  noise,
  snthresh,
  ppm,
  expandrt,
  binsize,
  minFraction,
  bw,
  annotation = "camera",
  cliqsamp = NA,
  mergepeaks = TRUE,
  rtadjust = TRUE,
  group = TRUE,
  fill = TRUE
)

Arguments

object	A OnDiskMSnExp/MSnExp object
polarity	A string indicating the polarity of the experiment "positive" or "negative"
groupvar	A string or numeric indicating the group variable used to group features
peakwidth	A two length numeric vector indicating the width of a peak
noise	A numeric indicating the maximum noise of a chromatographic
snthresh	A numeric indicating the minimum signal to noise ratio of a chromatographic peak
ppm	A numeric indicating the ppm error of the instrument
expandrt	A numeric indicating the RT seconds to search for overlapping peaks
binsize	A numeric indicating the binsize to perform RT adjusting
minFraction	A numeric indicating the minimum fraction of peaks to group features
bw	A numeric indicating the binwidth to group features.
annotation	A string indicating the annotation methodology. One of: "cliqueMS", "camera" or "none".
cliqsamp	A numeric indicating the sample from wich the cliqueMS annotation will be perform. Usually a pool QC sample.
mergepeaks	A boolean indicating if peak merging will be perform
rtadjust	A boolean indicating if retention time adjustment will be perform
group	A boolean indicating if peak grouping will be perform
fill	A boolean indicating if peak filling will be perform

Value

A processed XCMSnExp object, a annotation object if annotation was selected and a SummarizedExperiment with feature information.

Author(s)

Jordi Rofes Herrera

jordirofes/OmniOmics documentation built on Nov. 22, 2022, 5:46 a.m.