R: Accessing mz-rt feature data values

featureValues,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.

Usage

## S4 method for signature 'XCMSnExp'
featureValues(object, method = c("medret", "maxint"),
  value = "index", intensity = "into", filled = TRUE)

Arguments

`object`	A `XCMSnExp` object providing the feature definitions.
`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.
`value`	`character` specifying the name of the column in `chromPeaks(object)` that should be returned or `"index"` (the default) to return the index of the peak in the `chromPeaks(object)` matrix corresponding to the representative peak for the feature in the respective sample.
`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.

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).

Note

This method is equivalent to the groupval for xcmsSet objects.

Author(s)

Johannes Rainer