groupFeatures-abundance-correlation {xcms} | R Documentation |
Features from the same originating compound are expected to have similar
intensities across samples. This method this groups features based on
similarity of abundances (i.e. feature values) across samples.
See also AbundanceSimilarityParam()
for additional information and details.
This help page lists parameters specific for xcms
result objects (i.e. the
XCMSnExp()
object). Documentation of the parameters for the similarity
calculation is available in the AbundanceSimilarityParam()
help page in
the MsFeatures
package.
## S4 method for signature 'XCMSnExp,AbundanceSimilarityParam' groupFeatures( object, param, msLevel = 1L, method = c("medret", "maxint", "sum"), value = "into", intensity = "into", filled = TRUE, ... )
object |
|
param |
|
msLevel |
|
method |
|
value |
|
intensity |
|
filled |
|
... |
additional parameters passed to the |
input XCMSnExp
with feature group definitions added to a column
"feature_group"
in its featureDefinitions
data frame.
Johannes Rainer
feature-grouping for a general overview.
Other feature grouping methods:
groupFeatures-eic-similarity
,
groupFeatures-similar-rtime
library(MsFeatures) ## Load a test data set with detected peaks data(faahko_sub) ## Update the path to the files for the local system dirname(faahko_sub) <- system.file("cdf/KO", package = "faahKO") ## Disable parallel processing for this example register(SerialParam()) ## Group chromatographic peaks across samples xodg <- groupChromPeaks(faahko_sub, param = PeakDensityParam(sampleGroups = rep(1, 3))) ## Group features based on correlation of feature values (integrated ## peak area) across samples. Note that there are many missing values ## in the feature value which influence grouping of features in the present ## data set. xodg_grp <- groupFeatures(xodg, param = AbundanceSimilarityParam(threshold = 0.8)) table(featureDefinitions(xodg_grp)$feature_group) ## Group based on the maximal peak intensity per feature xodg_grp <- groupFeatures(xodg, param = AbundanceSimilarityParam(threshold = 0.8, value = "maxo")) table(featureDefinitions(xodg_grp)$feature_group)