feature_values: Feature table
In sipss/AlpsLCMS: Signal processing of LC-MS metabolomics

Description Usage Arguments Value Author(s) See Also

feature_values is a wrapper from xcms. The function creates an intensity matrix with all the features.

feature_values(
object,
method = c("medret", "maxint", "sum"),
value = "into",
intensity = "into",
filled = TRUE,
missing = NA,
msLevel = integer()
)

...

For quantify: additional parameters to be passed on to the featureValues method.

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.

Johannes Rainer

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.

sipss/AlpsLCMS documentation built on May 13, 2021, 6:18 p.m.