OptiLCMS: Optimized LC-MS Spectra Processing

Description Usage Arguments Value Examples

This functionn creates an extracted ion chromatogram (XIC/EIC) for a specific m/z and retention time. This is used for quality-control of raw m/s data.

PlotXIC(
  mSet = NULL,
  featureNum,
  sample_labeled,
  Group_labeled,
  format,
  dpi,
  width,
  height,
  sample_filled,
  group_filled
)

`mSet`	mSet Object. Should contain the spectra processing result.
`featureNum`	Numeric, Feature number in the feature table.
`sample_labeled`	Logical, whether to lable the sample name.
`Group_labeled`	Logical, whether to lable the group name.
`format`	Character, to give the format of BPI figures ploted. Can be "jpeg", "png", "pdf", "svg", "tiff" or "ps". Default is "png".
`dpi`	Numeric, to define the dpi of the figures. Default is 72.
`width`	Numeric, to define the width of the figure.
`height`	Numeric, to define the height of the figure.
`sample_filled`	Logical, to determine the EIC/XIC is filled or not for sample EIC
`group_filled`	Logical, to determine the EIC/XIC is filled or not for group EIC

will return a figure of EIC/XIC

data(mSet);
newPath <- dir(system.file("mzData", package = "mtbls2"),
               full.names = TRUE, recursive = TRUE)[c(10, 11, 12)]
mSet <- updateRawSpectraPath(mSet, newPath);
#PlotXIC(mSet, 1, TRUE, TRUE);