
Metaboprep Object
class_metaboprep.Rd
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).
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.