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A `Metaboprep` object is a container for matrices of metabolite data, along with associated metadata. It allows for efficient storage and manipulation of data, supporting quality control, transformations, and various analyses. This object facilitates easy access to data layers, sample and feature summaries, outlier treatment, and more.

Usage

Metaboprep(
  data,
  samples,
  features,
  exclusions = list(samples = list(user_excluded = character(),
    extreme_sample_missingness = character(), user_defined_sample_missingness =
    character(), user_defined_sample_totalpeakarea = character(),
    user_defined_sample_pca_outlier = character()), features = list(user_excluded =
    character(), extreme_feature_missingness = character(),
    user_defined_feature_missingness = character())),
  feature_summary = array(data = NA_real_, dim = c(0, 0, 0)),
  sample_summary = array(data = NA_real_, dim = c(0, 0, 0))
)

Arguments

data

numeric matrix, the data matrix containing metabolite values (not to be set directly).

samples

data.frame, a data frame containing sample-related information (not to be set directly).

features

data.frame, a data frame containing feature-related information (not to be set directly).

exclusions

list, holds exclusion codes for data masking (not to be set directly).

feature_summary

numeric matrix, summary statistics for features (not to be set directly).

sample_summary

numeric matrix, summary statistics for samples (not to be set directly).

Value

An object of class `Metaboprep` (S7 class).

Slots

data

numeric matrix, the metabolite data.

samples

data.frame, the samples data frame

features

data.frame, the features data frame

exclusions

list, exclusion codes (mask for data).

feature_summary

numeric matrix, feature summary statistics.

sample_summary

numeric matrix, sample summary statistics.