AnalysisParameters: Analysis parameters
In wolski/prolfqua: Proteomics Label Free Quantification

AnalysisParameters

R Documentation

Analysis parameters

Description

Analysis parameters

Public fields

qVal_individual_threshold: qValue threshold for sample
qVal_experiment_threshold: qValue threshold for dataset
qVal_minNumber_below_experiment_threshold: how many samples need to meet qVal_experiment_threshold
min_nr_of_notNA: minimum number of not NA's in all samples default 1
min_nr_of_notNA_condition: minimum number of not NA's in interaction
min_peptides_protein: minimum number of peptides per protein

Methods

Public methods

AnalysisParameters$clone()

Method `clone()`

The objects of this class are cloneable with this method.

Usage

AnalysisParameters$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.

Other configuration: AnalysisConfiguration, AnalysisTableAnnotation, INTERNAL_FUNCTIONS_BY_FAMILY, R6_extract_values(), complete_cases(), concrete_AnalysisConfiguration, make_interaction_column(), make_reduced_hierarchy_config(), sample_subset(), separate_factors(), separate_hierarchy(), setup_analysis(), spread_response_by_IsotopeLabel(), table_factors(), table_factors_size()