
Feature Summary Statistics
feature_summary.Rd
This function estimates feature statistics for samples in a matrix of metabolite features.
Usage
feature_summary(
metaboprep,
source_layer = "input",
outlier_udist = 5,
tree_cut_height = 0.5,
sample_ids = NULL,
feature_ids = NULL,
features_exclude = NULL,
output = "data.frame"
)
Arguments
- metaboprep
an object of class Metabolites
- source_layer
character, the data layer to summarise
- outlier_udist
the unit distance in SD or IQR from the mean or median estimate, respectively outliers are identified at. Default value is 5.
- tree_cut_height
numeric, the threshold for feature independence in hierarchical clustering. Default is 0.5.
- sample_ids
character, vector of sample ids to work with
- feature_ids
character, vector of feature ids to work with
- features_exclude
character, vector of feature id indicating features to exclude from the sample and PCA summary analysis but keep in the data
- output
character, type of output, either 'object' to return the updated metaboprep object, or 'data.frame' to return the data.