processing options R6 class
Description
processing options R6 class
processing options R6 class
Public fields
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transform - data transformation method
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aggregate - protein abundance estimation method
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diff_threshold - difference threshold
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FDR_threshold - FDR threshold
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remove_cont - should contaminants be removed
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remove_decoys - should decoys be removed
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pattern_decoys - decoy patterns
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pattern_contaminants - pattern contaminants
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nr_peptides - number of peptides
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interaction - model with interactions default FALSE
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model_missing - model missigness, default TRUE
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model - facade registry key for contrast analysis. Valid keys include prolfqua facade keys such as lm, lm_missing, lm_impute, limma, limma_impute, rlm, deqms, firth, lmer, ropeca, plus the prolfquasaint-backed key saint. Default "lm_impute".
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other - list with additional options
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internal - protein IDs for internal standard normalization e.g. ‘internal: [P01876, P02768]’ After transformation, intensities are centered relative to these proteins.
Methods
Public methods
Method clone()
The objects of this class are cloneable with this method.
Usage
ProcessingOptions\$clone(deep = FALSE)
Arguments
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deep - Whether to make a deep clone.
See Also
Other ProlfquAppConfig: ExternalReader, ProjectSpec, ProlfquAppConfig, make_DEA_config_R6(), set_list_to_R6()