Accessing mz-rt feature data values

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::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 class 'XCMSnExp'
quantify(object, ...)

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

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::SummarizedExperiment() representing the preprocessing results.

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.

Author

Johannes Rainer