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Find EICs that behave like contaminants

Source: R/contaminants_untargeted.R
EIC_contaminants.Rd

This function looks in raw LC-MS data for "features"/EICs that behave like contaminants. Behaving like contaminants in this case means that a certain m/z values is present in more than min_time above intensity min_int.

Usage

EIC_contaminants(
  raw,
  bin_ppm = 30,
  interval_ppm = 30,
  min_time = 5,
  merge_corr = 0.9,
  merge_ppm = 30,
  min_int = 5000
)

Arguments

raw

xcmsRaw object to profile

bin_ppm

Tolerance (ppm) for initial binning of m/z values

interval_ppm

Tolerance for creating final EICs after merging similar bins

min_time

Minimum time (minutes) an EIC should be above min_int to be considered a contaminant.

merge_corr

Minimum correlation between EICs to be merged.

merge_ppm

Maximum difference (ppm) between EICs to be merged.

min_int

Minimum intensity that the EIC needs to be above for a a minimum of min_time.

Value

A tibble containing the columns:

  • mz: m/z of the proposed contaminant

  • EIC: EIC of the m/z.