CITRUS-class {CytobankAPI}

S4 CITRUS Class

Description

A CITRUS object that holds pertinent CITRUS advanced analysis run information, learn more about CITRUS. This class should never be called explicitly. If a user would like to create a new Cytobank CITRUS object, utilize the citrus.new function, or any other CITRUS endpoints that return CITRUS objects documented in the 'Details' section.

Value

A CITRUS advanced analysis object

Slots

associated_models

list representing statistical methods used to discover stratifying signatures from clustered data features that explain differences between sample groups, learn more about CITRUS association models
- choose from the following : ("sam", "pamr" [default], "glmnet")

attachment_id

numeric representing the CITRUS attachment ID

cross_validation_folds

numeric representing the regulation threshold, controlling the number of features in the model (only applies to PAM, LASSO), learn more about CITRUS cross validation folds

citrus_id

numeric representing the CITRUS analysis ID

cluster_characterization

character representing the principle for analyzing and quantifying individual samples, learn more about CITRUS cluster characterization
- choose one of the following : ("abundance" [default], "medians")

event_sampling_method

character representing the sampling method, learn more about CITRUS event sampling methods
- choose one of the following : ("equal" [default], "max-per-file")

events_per_file

numeric representing the number of events taken from each sample

false_discovery_rate

numeric representing the false discovery rate (only applies to PAM, SAM), learn more about CITRUS false discovery rate

file_grouping

numeric dataframe representing which group samples belong to, learn more about CITRUS file grouping, the core functionality of CITRUS

minimum_cluster_size

numeric representing the number of nodes, learn more about CITRUS minimum cluster size

normalize_scales

logical representing whether or not to normalize channels, learn more about normalizing CITRUS scales

plot_theme

character representing the background color of images and figures within the CITRUS results
- choose one of the following : ("white" [default], "black")

population_id

dataframe representing a population gate set ID

statistics_channels

list representing the statistics channels used for the 'median' cluster characterization, these channels should not be selected for clustering