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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.