DataLoaderVariantGemini: loader corresponding to GEMINI files • May need to use...

In Paradigm4/revealgenomics: SciDB REVEAL/Genomics API

Description

loader corresponding to GEMINI files

• May need to use feature-synonym for feature matching, but current implementation is inefficient

• also has hard-coded links to column names used for feature matching (e.g. gene)

loader corresponding to GEMINI files

• May need to use feature-synonym for feature matching, but current implementation is inefficient

• also has hard-coded links to column names used for feature matching (e.g. gene)

Super classes

revealgenomics::DataLoader -> revealgenomics::DataLoaderVariant -> DataLoaderVariantGemini

Methods

Public methods

• DataLoaderVariantGemini$print_level()

• DataLoaderVariantGemini$assign_feature_ids()

• DataLoaderVariantGemini$register_new_features()

• DataLoaderVariantGemini$clone()

Inherited methods

• revealgenomics::DataLoader$assign_biosample_ids()

• revealgenomics::DataLoader$assign_other_ids()

• revealgenomics::DataLoader$download_features_for_featureset()

• revealgenomics::DataLoader$initialize()

• revealgenomics::DataLoader$retrieve_feature_synonyms()

• revealgenomics::DataLoader$retrieve_features()

• revealgenomics::DataLoader$returnReferenceObject()

• revealgenomics::DataLoader$update_reference_object()

• revealgenomics::DataLoaderVariant$load_data()

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Method print_level()

Usage

DataLoaderVariantGemini$print_level()

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Method assign_feature_ids()

Usage

DataLoaderVariantGemini$assign_feature_ids()

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Method register_new_features()

Usage

DataLoaderVariantGemini$register_new_features()

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Method clone()

The objects of this class are cloneable with this method.

Usage

DataLoaderVariantGemini$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Paradigm4/revealgenomics documentation built on April 7, 2020, 2:01 a.m.