Obtains extracted ion chromatograms (EICs) — getEICs-methods • patRoon

These methods generate one or more EIC(s). The data.table and data.frame methods generate EIC(s) for given retention time, m/z and optionally mobility ranges. The features and featureGroups methods generate EICs for all (or selected) features and feature groups, respectively, whereby the ranges are automatically determined from the feature data (see the EIC parameters for configuration options).

Usage

# S4 method for class 'features'
getEICs(
  obj,
  analysis = analyses(obj),
  EICParams = getDefEICParams(),
  output = "fill"
)

# S4 method for class 'featureGroups'
getEICs(
  obj,
  analysis = analyses(obj),
  groupName = names(obj),
  EICParams = getDefEICParams(),
  output = "fill"
)

# S4 method for class 'data.table'
getEICs(obj, ranges, gapFactor = 3, output = "fill", minIntensityIMS = 25)

# S4 method for class 'data.frame'
getEICs(obj, ...)

Arguments

obj: For the data.table and data.frame methods: a table with analysis information. For the features and featureGroups methods: the object for which EICs should be generated.
analysis: A character vector with the analyses for which EICs should be generated.
EICParams: A named list with parameters used for extracted ion chromatogram (EIC) creation. See the EIC parameters documentation 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.
groupName: A character vector with the names of the feature groups for which EICs should be generated.
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.
minIntensityIMS: (IMS workflow) Raw intensity threshold for IMS data. This is primarily intended to speed up raw data processing.
...: For the data.frame method: further arguments passed to the data.table method.

Value

A list with for each analysis a list with EIC data. For the data.table and data.frame methods the EICs are ordered according to the rows in ranges. For the features and featureGroups methods the EICs are named after the feature IDs and feature group names, respectively, and analyses without any EIC data are omitted.

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.

Functions

getEICs(features): Generates EICs for all (or selected) features (method for features).
getEICs(featureGroups): Generates EICs for all (or selected) feature groups (method for featureGroups).
getEICs(data.table): Generates one or more EIC(s) for given retention time, m/z and optionally mobility ranges (method for data.table).
getEICs(data.frame): Wrapper for the data.table method (method for data.frame).

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.