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Report feature group data (legacy interface)

Source: R/generics.R, R/report-legacy.R
reporting-legacy.Rd

Functionality to report data produced by most workflow steps such as features, feature groups, calculated chemical formulae and tentatively identified compounds. This is the legacy interface, for the updated interface see reporting.

Usage

reportCSV(
  fGroups,
  path = "report",
  reportFeatures = FALSE,
  formulas = NULL,
  formulasNormalizeScores = "max",
  formulasExclNormScores = NULL,
  compounds = NULL,
  compoundsNormalizeScores = "max",
  compoundsExclNormScores = c("score", "individualMoNAScore", "annoTypeCount",
    "annotHitCount", "libMatch"),
  compsCluster = NULL,
  components = NULL,
  retMin = TRUE,
  clearPath = FALSE
)

reportPDF(
  fGroups,
  path = "report",
  reportFGroups = TRUE,
  formulas = NULL,
  formulasTopMost = 5,
  formulasNormalizeScores = "max",
  formulasExclNormScores = NULL,
  reportFormulaSpectra = TRUE,
  compounds = NULL,
  compoundsNormalizeScores = "max",
  compoundsExclNormScores = c("score", "individualMoNAScore", "annoTypeCount",
    "annotHitCount", "libMatch"),
  compoundsOnlyUsedScorings = TRUE,
  compoundsTopMost = 5,
  compsCluster = NULL,
  components = NULL,
  MSPeakLists = NULL,
  retMin = TRUE,
  EICGrid = c(2, 1),
  EICParams = getDefEICParams(window = 20, topMost = 1, topMostByReplicate = TRUE),
  clearPath = FALSE
)

# S4 method for class 'featureGroups'
reportCSV(
  fGroups,
  path = "report",
  reportFeatures = FALSE,
  formulas = NULL,
  formulasNormalizeScores = "max",
  formulasExclNormScores = NULL,
  compounds = NULL,
  compoundsNormalizeScores = "max",
  compoundsExclNormScores = c("score", "individualMoNAScore", "annoTypeCount",
    "annotHitCount", "libMatch"),
  compsCluster = NULL,
  components = NULL,
  retMin = TRUE,
  clearPath = FALSE
)

# S4 method for class 'featureGroups'
reportPDF(
  fGroups,
  path = "report",
  reportFGroups = TRUE,
  formulas = NULL,
  formulasTopMost = 5,
  formulasNormalizeScores = "max",
  formulasExclNormScores = NULL,
  reportFormulaSpectra = TRUE,
  compounds = NULL,
  compoundsNormalizeScores = "max",
  compoundsExclNormScores = c("score", "individualMoNAScore", "annoTypeCount",
    "annotHitCount", "libMatch"),
  compoundsOnlyUsedScorings = TRUE,
  compoundsTopMost = 5,
  compsCluster = NULL,
  components = NULL,
  MSPeakLists = NULL,
  retMin = TRUE,
  EICGrid = c(2, 1),
  EICParams = getDefEICParams(),
  clearPath = FALSE
)

Arguments

fGroups

The featureGroups object that should be used for reporting data.

path

The destination file path for files generated during reporting. Will be generated if needed.

reportFeatures

If set to TRUE then for each analysis a .csv file will be generated with information about its detected features.

formulas, compounds, compsCluster, components

Further objects (formulas, compounds, compoundsCluster, components) that should be reported. Specify NULL to skip reporting a particular object.

compoundsNormalizeScores, formulasNormalizeScores

A character that specifies how normalization of annotation scorings occurs. Either "none" (no normalization), "max" (normalize to max value) or "minmax" (perform min-max normalization). Note that normalization of negative scores (e.g. output by SIRIUS) is always performed as min-max. Furthermore, currently normalization for compounds takes the original min/max scoring values into account when candidates were generated. Thus, for compounds scoring, normalization is not affected when candidate results were removed after they were generated (e.g. by use of filter).

compoundsExclNormScores, formulasExclNormScores

A character vector specifying any compound scoring names that should not be normalized. Set to NULL to normalize all scorings. Note that whether any normalization occurs is set by the compoundsExclNormScores,formulasExclNormScores argument.

For compounds: By default score and individualMoNAScore are set to mimic the behavior of the MetFrag web interface.

retMin

If TRUE then report retention times in minutes (otherwise seconds).

clearPath

If TRUE then the destination path will be (recursively) removed prior to reporting.

reportFGroups

If TRUE then feature group data will be reported.

formulasTopMost, compoundsTopMost

Only this amount of top ranked candidate formulae/compounds are reported. Lower values may significantly speed up reporting. Set to NULL to ignore.

reportFormulaSpectra

If TRUE then explained MS/MS spectra (if available) for candidate formulae will be reported. Specifying formulas and setting this argument to FALSE still allows further annotation of compound MS/MS spectra.

compoundsOnlyUsedScorings

If TRUE then only scorings are plotted that actually have been used to rank data (see the scoreTypes argument to generateCompoundsMetFrag for more details).

MSPeakLists

A MSPeakLists object that is mandatory when spectra for formulae and/or compounds will be reported.

EICGrid

An integer vector in the form c(columns, rows) that is used to determine the plotting grid when reporting EICs in PDF files.

EICParams

A named list with parameters used for extracted ion chromatogram (EIC) creation. See the EIC parameters documentation for more details.

Details

These functions are usually called at the very end of the workflow. It is used to report various data on features and feature groups. In addition, these functions may be used for reporting formulae and/or compounds that were generated for the specified feature groups. Data can be reported in tabular form (i.e. .csv files) by reportCSV or graphically by reportPDF and reportHTML. The latter functions will plot for instance chromatograms and annotated mass spectra, which are useful to get a graphical overview of results.

All functions have a wide variety of arguments that influence the reporting process. Nevertheless, most parameters are optional and only required to be given for fine tuning. In addition, only those objects (e.g. formulae, compounds, clustering) that are desired to be reported need to be specified.

reportCSV generates tabular data (i.e. .csv files) for given data to be reported. This may also be useful to allow import by other tools for post processing.

reportPDF will report graphical data (e.g. chromatograms and mass spectra) within PDF files. Compared to reportHTML this function may be faster and yield smaller report files, however, its functionality is a bit more basic and generated data is more 'scattered' around.

Note

Any formulae and compounds for feature groups which are not present within fGroups (i.e. because it has been subset afterwards) will not be reported.

The topMost, topMostByReplicate and onlyPresent EIC parameters may be ignored, e.g., when generating overview plots.

Use of raw HRMS data

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

See also

reporting