DataReaderVariantFormatA: generic variant loader that aims to work with multiple...

In Paradigm4/revealgenomics: SciDB REVEAL/Genomics API

Description

generic variant loader that aims to work with multiple formats

• makes sure the mandatory fields for registering variants are named accordingly

• for biosample matching, preps a column called biosample_name

• for feature matching

  • creates a column called scidb_feature_column

  • stores annotation information in feature_annotation_df slot (column name of this data.frame describes whether feature name or gene_symbol should be used for matching)

generic variant loader that aims to work with multiple formats

• makes sure the mandatory fields for registering variants are named accordingly

• for biosample matching, preps a column called biosample_name

• for feature matching

  • creates a column called scidb_feature_column

  • stores annotation information in feature_annotation_df slot (column name of this data.frame describes whether feature name or gene_symbol should be used for matching)

Super classes

revealgenomics::DataReader -> revealgenomics::DataReaderVariant -> DataReaderVariantFormatA

Methods

Public methods

• DataReaderVariantFormatA$print_level()

• DataReaderVariantFormatA$load_data_from_file()

• DataReaderVariantFormatA$clone()

Inherited methods

• revealgenomics::DataReader$enforce_data_file_sample_name_column()

• revealgenomics::DataReader$file_format_handler()

• revealgenomics::DataReader$get_data()

• revealgenomics::DataReader$get_feature_annotation()

• revealgenomics::DataReader$initialize()

• revealgenomics::DataReader$transpose_matrix_if_required()

• revealgenomics::DataReader$verify_read()

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Method print_level()

Usage

DataReaderVariantFormatA$print_level()

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Method load_data_from_file()

Usage

DataReaderVariantFormatA$load_data_from_file()

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Method clone()

The objects of this class are cloneable with this method.

Usage

DataReaderVariantFormatA$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

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