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Plot extracted ion chromatograms from raw mzML/mzXML data

Source: R/plotEIC.R
plotEIC.Rd

Reads mzML/mzXML raw data and plots extracted ion chromatograms (EIC) for a list of target m/z values at MS1 or MS2 level. Uses RaMS for lightweight data access and plotly for interactive visualization.

Usage

plotEIC(filepath, featlist, diff = 0.005)

Arguments

filepath

character. Path to an mzML or mzXML file.

featlist

data.frame with columns: name (feature label), mz (target m/z), ms_level (either "ms1" or "ms2").

diff

numeric. Half-width of the m/z extraction window in Da. Default 0.005.

Value

A plotly object with overlaid extracted ion chromatograms.

Examples

if (FALSE) { # \dontrun{
featlist <- data.frame(
  name = c("target1", "target2"),
  mz = c(300.1234, 350.5678),
  ms_level = c("ms1", "ms2")
)
plotEIC("sample.mzML", featlist)
} # }