Base features class

Holds information for all features present within a set of analysis.

# S4 method for class 'features'
length(x)

# S4 method for class 'features'
show(object)

# S4 method for class 'features'
featureTable(obj)

# S4 method for class 'features'
analysisInfo(obj, df = FALSE)

# S4 method for class 'features'
getFeatureQualityNames(obj, scores = FALSE, totScore = TRUE)

# S4 method for class 'features'
analysisInfo(obj) <- value

# S4 method for class 'features'
analyses(obj)

# S4 method for class 'features'
replicates(obj)

# S4 method for class 'features'
hasIMS(obj)

# S4 method for class 'features'
fromIMS(obj)

# S4 method for class 'features'
as.data.table(x)

# S4 method for class 'features'
filter(
  obj,
  absMinIntensity = NULL,
  relMinIntensity = NULL,
  retentionRange = NULL,
  mzRange = NULL,
  mzDefectRange = NULL,
  chromWidthRange = NULL,
  IMSRangeParams = NULL,
  qualityRange = NULL,
  negate = FALSE
)

# S4 method for class 'features,ANY,missing,missing'
x[i, j, ..., ni, reorder = FALSE, drop = TRUE]

# S4 method for class 'features,ANY,missing'
x[[i]]

# S4 method for class 'features'
x$name

# S4 method for class 'features'
delete(obj, i = NULL, j = NULL, ...)

# S4 method for class 'features'
calculatePeakQualities(
  obj,
  weights,
  flatnessFactor,
  featureQualities = NULL,
  EICParams = getDefEICParams(window = 0),
  parallel = TRUE
)

# S4 method for class 'features'
getTICs(obj, retentionRange = NULL, MSLevel = 1)

# S4 method for class 'features'
getBPCs(obj, retentionRange = NULL, MSLevel = 1)

# S4 method for class 'features'
plotTICs(
  obj,
  retentionRange = NULL,
  MSLevel = 1,
  retMin = FALSE,
  title = NULL,
  groupBy = NULL,
  showLegend = TRUE,
  xlim = NULL,
  ylim = NULL,
  ...
)

# S4 method for class 'features'
plotBPCs(
  obj,
  retentionRange = NULL,
  MSLevel = 1,
  retMin = FALSE,
  title = NULL,
  groupBy = NULL,
  showLegend = TRUE,
  xlim = NULL,
  ylim = NULL,
  ...
)

# S4 method for class 'featuresSet'
sets(obj)

# S4 method for class 'featuresSet'
show(object)

# S4 method for class 'featuresSet'
as.data.table(x)

# S4 method for class 'featuresSet,ANY,missing,missing'
x[i, ..., sets = NULL, reorder = FALSE, drop = TRUE]

# S4 method for class 'featuresSet'
filter(obj, ..., negate = FALSE, sets = NULL)

# S4 method for class 'featuresSet'
unset(obj, set)

# S4 method for class 'featuresKPIC2'
delete(obj, i = NULL, j = NULL, ...)

# S4 method for class 'featuresPiek'
delete(obj, i = NULL, j = NULL, ...)

# S4 method for class 'featuresXCMS'
analysisInfo(obj) <- value

# S4 method for class 'featuresXCMS'
delete(obj, i = NULL, j = NULL, ...)

# S4 method for class 'featuresXCMS3'
delete(obj, i = NULL, j = NULL, ...)

Arguments

obj, x, object

features object to be accessed

df

If TRUE then the returned value is a data.frame, otherwise a data.table.

scores

If TRUE the score names are returned, otherwise the quality names.

totScore

If TRUE (and scores=TRUE) then the name of the total score is included.

value

A data.frame or data.table with the new analysis information.

absMinIntensity, relMinIntensity

Minimum absolute/relative intensity for features to be kept. The relative intensity is determined from the feature with highest intensity (within the same analysis). Set to 0 or NULL to skip this step.

retentionRange, mzRange, mzDefectRange, chromWidthRange

Range of retention time (in seconds), m/z, mass defect (defined as the decimal part of m/z values) or chromatographic peak width (in seconds), respectively. Features outside this range will be removed. Should be a numeric vector with length of two containing the min/max values. The maximum can be Inf to specify no maximum range. Set to NULL to skip this step.

IMSRangeParams

(IMS workflow) A list with parameters to be used for filtering IMS range data. See getIMSRangeParams for details and how to make such a parameter list.

qualityRange

Used to filter features by their peak qualities/scores (see calculatePeakQualities). Should be a named list with min/max ranges for each quality/score to be filtered (the getFeatureQualityNames function can be used to obtain valid names). Example: qualityRange=list(ModalityScore=c(0.3, Inf), SymmetryScore=c(0.5, Inf)). Set to NULL to ignore.

negate

If set to TRUE then filtering operations are performed in opposite manner.

i, j

For [/[[: A numeric or character value which is used to select analyses by their index or name, respectively (for the order/names see analyses()).

For [: Can also be logical to perform logical selection (similar to regular vectors). If missing all analyses are selected.

For [[: should be a scalar value.

For delete: The data to remove from. i are the analyses as numeric index, logical or character, j the features as numeric index (row) of the feature. If either is NULL then data for all is removed. j may also be a function: it will be called for each analysis, with the feature table (a data.table), the analysis name and any other arguments passed as ... to delete. The return value of this function specifies the feature indices (rows) to be removed (specified as an integer or logical vector).

...

For delete: passed to the function specified as j.

For plotTICs and plotBPCs: further arguments passed to plot.

For sets workflow methods: further arguments passed to the base features method.

ni

Optional argument. An expression used for subsetting the analyses. The analysis information is first subset and the remaining rows are used to determine for which analyses the results should be kept. The unevaluated ni expression is used to set the i argument of the subset operator of data.table, which therefore brings the advanced subsetting capabilities of data.table (see the data.table documentation for more details). For instance, fList[replicate == "standard"] would subset all analyses assigned with the replicate "standard".

reorder

If TRUE then the order of the analyses is changed to match the order of the i argument.

(sets workflow) If the sets argument is specified (and i is not) then the order of sets is changed instead.

drop

Ignored.

name

The analysis name (partially matched).

weights

A named numeric vector that defines the weight for each score to calculate the totalScore. The names of the vector follow the score names. Unspecified weights are defaulted to 1. Example: weights=c(ApexBoundaryRatioScore=0.5, GaussianSimilarityScore=2).

flatnessFactor

Passed to MetaClean as the flatness.factor argument to calculateJaggedness and calculateModality.

featureQualities

Specifies which feature qualities to calculate. Can be NULL (default, calculates all qualities), a character vector with names of qualities to calculate (e.g., c("FWHM2Base", "Symmetry")), or a list of custom quality definitions. See the featureQualities function for more details.

EICParams

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

parallel

If set to TRUE then code is executed in parallel through the future package. Please see the parallelization section in the handbook for more details.

MSLevel

Integer vector with the ms levels (i.e., 1 for MS1 and 2 for MS2) to obtain traces.

retMin

Plot retention time in minutes (instead of seconds).

title

Character string used for title of the plot. If NULL a title will be automatically generated.

groupBy

Specifies how results are grouped in the plot. Should be a name of a column in the analysis information table which is used to make analysis groups (e.g. "replicate"), or "fGroups" to group by feature group. Set to NULL for no grouping.

showLegend

Plot a legend if TRUE.

xlim, ylim

Sets the plot size limits used by plot. Set to NULL for automatic plot sizing.

sets

(sets workflow) For [ and filter: a character with name(s) of the sets to keep (or remove if negate=TRUE).

set

(sets workflow) The name of the set.

Value

featureTable: A list containing a data.table for each analysis with feature data

analysisInfo: The analysis information of this features object.

delete returns the object for which the specified data was removed.

calculatePeakQualities returns a modified object amended with peak qualities and scores.

Details

This class provides a way to store intensity, retention times, m/z and other data for all features in a set of analyses. The class is virtual and derived objects are created by 'feature finders' such as findFeaturesOpenMS, findFeaturesXCMS and findFeaturesBruker.

Methods (by generic)

• length(features): Obtain total number of features.

• show(features): Shows summary information for this object.

• featureTable(features): Get table with feature information

• analysisInfo(features): Get analysis information

• getFeatureQualityNames(features): Returns the present chromatographic peak quality and score names for features.

• analysisInfo(features) <- value: Modifies analysis information

• analyses(features): returns a character vector with the names of the analyses for which data is present in this object.

• replicates(features): returns a character vector with the names of the replicates for which data is present in this object.

• hasIMS(features): Returns TRUE if the features object has mobility information.

• fromIMS(features): Returns TRUE if the features object was directly created from IMS data.

• as.data.table(features): Returns all feature data in a table.

• filter(features): Performs common rule based filtering of features. Note that this (and much more) functionality is also provided by the filter method defined for featureGroups. However, filtering a features object may be useful to avoid grouping large amounts of features.

• x[i: Subset on analyses.

• x[[i: Extract a feature table for an analysis.

• $: Extract a feature table for an analysis.

• delete(features): Completely deletes specified features.

• calculatePeakQualities(features): Calculates peak qualities for each feature. Please see the featureQualities function and MetaClean publication (referenced below) for more details. For each metric, an additional score is calculated by normalizing all feature values (unless the quality metric definition has a fixed range) and scale from 0 (worst) to 1 (best). Then, a totalScore for each feature is calculated by the (weighted) sum of all score values.

• getTICs(features): Obtain the total ion chromatogram/s (TICs) of the analyses.

• getBPCs(features): Obtain the base peak chromatogram/s (BPCs) of the analyses.

• plotTICs(features): Plots the TICs of the analyses.

• plotBPCs(features): Plots the BPCs of the analyses.

Slots

features

List of features per analysis file. Use the featureTable method for access.

analysisInfo

A data.table with the analysis information. Use the analysisInfo method for access.

featureQualityNames

Character vector with the names of the chromatographic peak quality metrics that are present.

hasIMS

A logical that is TRUE if the features object contain mobility/CCS information. Use the hasIMS method for access.

fromIMS

A logical that is TRUE if the features object was directly created from IMS data (i.e. direct mobility assignment workflow). Use the fromIMS method for access.

Note

For calculatePeakQualities: sometimes MetaClean may return NA for the Gaussian Similarity and Symmetry metrics, in which case it will be set to 0.

S4 class hierarchy

• workflowStep

  • features

    • featuresSet

    • featuresUnset

    • featuresFromFeatGroups

    • featuresConsensus

    • featuresBruker

    • featuresEnviPick

    • featuresKPIC2

    • featuresOpenMS

    • featuresPiek

    • featuresSAFD

    • featuresSIRIUS

    • featuresTable

    • featuresBrukerTASQ

    • featuresXCMS

    • featuresXCMS3

Use of raw HRMS data

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

Sets workflows

The featuresSet class is applicable for sets workflows. This class is derived from features and therefore largely follows the same user interface.

The following methods are specifically defined for sets workflows:

• sets Returns the set names for this object.

• unset Converts the object data for a specified set into a 'non-set' object (featuresUnset), which allows it to be used in 'regular' workflows. The adduct annotations for the selected set (e.g. as passed to makeSet) are used to convert all feature masses to ionic m/z values.

The following methods are changed or with new functionality:

• filter and the subset operator ([) have specific arguments to choose/filter by (feature presence in) sets. See the sets argument description.

• Important: the mzRange, mzDefectRange and IMSRangeParams filters use neutral feature masses, whereas non-sets workflows use m/z values. Hence, adjust accordingly to avoid (slightly) different results!

References

Chetnik K, Petrick L, Pandey G (2020). “MetaClean: a machine learning-based classifier for reduced false positive peak detection in untargeted LC-MS metabolomics data.” Metabolomics, 16(11). doi:10.1007/s11306-020-01738-3 .

See also

findFeatures

Author

Rick Helmus <r.helmus@uva.nl> and Ricardo Cunha <cunha@iuta.de> (getTICs, getBPCs, plotTICs and plotBPCs functions)