featureValues,XCMSnExp-method | R Documentation |
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.
## S4 method for signature 'XCMSnExp'
featureValues(object, method = c("medret", "maxint",
"sum"), value = "into", intensity = "into", filled = TRUE,
missing = NA)
object |
A |
method |
|
value |
|
intensity |
|
filled |
|
missing |
how missing values should be reported. Allowed values are
|
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).
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
.
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.
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