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Obtains extracted ion chromatograms (EICs)

Source: R/utils-exported.R
getEICs.Rd

This function generates one or more EIC(s) for given retention time, m/z and optionally mobility ranges.

Usage

getEICs(
  analysisInfo,
  ranges,
  gapFactor = 3,
  output = "fill",
  minIntensityIMS = 25
)

Arguments

analysisInfo

A data.frame (or data.table) with Analysis information.

ranges

A list with for each analysis a data.frame with numeric columns "retmin", "retmax", "mzmin", "mzmax" with the lower/upper ranges of the retention time and m/z. Furthermore, columns "mobmin" and "mobmax" can be added for mobility lower/upper ranges in IMS data.

gapFactor

A numeric that configures gap filling. See getDefEICParams for more details.

output

Should be "fill", "pad" or "raw". Internally, EIC data is compressed by omitting any zero intensity data points. If output="fill" then the zero intensity points are re-added to obtain continuous chromatograms. If output="pad" then zero intensity points are only re-added that surround others, which is sufficient for e.g. plotting. If output="raw" then the original compressed data is returned.

minIntensityIMS

(IMS workflow) Raw intensity threshold for IMS data. This is primarily intended to speed up raw data processing.

Value

A list with for each analysis a list with EIC data for each of the rows in ranges.

If output="raw" then additional columns with e.g. mean-averaged and base peak m/z values for each data point are returned. Furthermore, the allXValues attribute is set that can be used to obtain the original retention time values to reconstruct the original complete chromatogram.

Use of raw HRMS data

The raw data interface of patRoon is used by getEICs to process HRMS (or IMS-HRMS) data. Please see its documentation for more information on the supported formats and available configuration options.