Summary Statistics — summarise • metaboprep

Summarise the sample and feature data

Usage

summarise(
  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 Metaboprep
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.