quantify,XCMSnExp-method {xcms} | R Documentation

## Accessing mz-rt feature data values

### Description

`featureValues,XCMSnExp` : extract a `matrix` for feature values with rows representing features and columns samples. Parameter `value` allows to define which column from the `chromPeaks` matrix should be returned. Multiple chromatographic peaks from the same sample can be assigned to a feature. Parameter `method` allows to specify the method to be used in such cases to chose from which of the peaks the value should be returned. Parameter 'msLevel' allows to choose a specific MS level for which feature values should be returned (given that features have been defined for that MS level).

`quantify,XCMSnExp`: return the preprocessing results as an `SummarizedExperiment` object containing the feature abundances as assay matrix, the feature definitions (returned by `featureDefinitions`) as `rowData` and the phenotype information as `colData`. This is an ideal container for further processing of the data. Internally, the `featureValues` method is used to extract the feature abundances, parameters for that method can be passed to `quantify` with `...`.

### Usage

    ## S4 method for signature 'XCMSnExp'
    quantify(object, ...)

    ## S4 method for signature 'XCMSnExp'
    featureValues(
      object,
      method = c("medret", "maxint", "sum"),
      value = "into",
      intensity = "into",
      filled = TRUE,
      missing = NA,
      msLevel = 1:20
    )

### Arguments

`object` | A `XCMSnExp` object providing the feature definitions.
`...` | For `quantify`: additional parameters to be passed on to the `featureValues` method.
`method` | `character` specifying the method to resolve multi-peak mappings within the same sample, i.e. to define the representative peak for a feature in samples where more than one peak was assigned to the feature. If `"medret"`: select the peak closest to the median retention time of the feature. If `"maxint"`: select the peak yielding the largest signal. If `"sum"`: sum the values (only if `value` is `"into"` or `"maxo"`.
`value` | `character` specifying the name of the column in `chromPeaks(object)` that should be returned. Defaults to `"into"` in which case the integrated peak area is returned. To get the index of the peak in the `chromPeaks(object)` matrix use `"index"`.
`intensity` | `character` specifying the name of the column in the `chromPeaks(objects)` matrix containing the intensity value of the peak that should be used for the conflict resolution if `method = "maxint"`.
`filled` | `logical(1)` specifying whether values for filled-in peaks should be returned or not. If `filled = FALSE`, an `NA` is returned in the matrix for the respective peak. See `fillChromPeaks` for details on peak filling.
`missing` | how missing values should be reported. Allowed values are `NA` (the default), a `numeric` or `missing = "rowmin_half"`. The latter replaces any `NA` with half of the row's minimal (non-missing) value.
`msLevel` | for 'featureValues': 'integer' defining the MS level(s) for which feature values should be returned. By default, values for features defined for all MS levels are returned.

### Value

For `featureValues`: a `matrix` with feature values, columns representing samples, rows features. The order of the features matches the order found in the `featureDefinitions(object)` `DataFrame`. The rownames of the `matrix` are the same than those of the `featureDefinitions` `DataFrame`. `NA` is reported for features without corresponding chromatographic peak in the respective sample(s).

For `quantify`: a `SummarizedExperiment` representing the preprocessing results.

### Note

This method is equivalent to the `groupval` for `xcmsSet` objects. Note that `missing = 0` should be used to get the same behaviour as `groupval`, i.e. report missing values as 0 after a call to `fillPeaks`.

### Author(s)

Johannes Rainer

### See Also

`XCMSnExp` for information on the data object.

`featureDefinitions` to extract the `DataFrame` with the feature definitions.

`featureChromatograms` to extract ion chromatograms for each feature.

`hasFeatures` to evaluate whether the `XCMSnExp` provides feature definitions.

`groupval` for the equivalent method on `xcmsSet` objects.

[Package xcms version 3.10.2 Index]