PicSureHpdsDictionaryBdc: PicSureHpdsDictionaryBdc

In hms-dbmi/pic-sure-biodatacatalyst-r-adapter-hpds: Simplified R library to communicate with HPDS-hosted services on the BioData Catalyst network

PicSureHpdsDictionaryBdc

Description

R6 class that runs searches against a HPDS resource's data dictionary - DO NOT CREATE THIS OBJECT DIRECTLY!

For full documentation of each method go to https://github.com/hms-dbmi/pic-sure-r-adapter-hpds

Value

Object of R6Class used to access a HPDS-hosted resource's data dictionary.

Methods

Public methods

• PicSureHpdsDictionaryBdc$new()

• PicSureHpdsDictionaryBdc$getKeyInfo()

• PicSureHpdsDictionaryBdc$genotypeAnnotations()

• PicSureHpdsDictionaryBdc$find()

• PicSureHpdsDictionaryBdc$clone()

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Method new()

This method is used to create new PicSureHpdsDictionaryBdc object. DO NOT CREATE THIS OBJECT DIRECTLY!

Usage

PicSureHpdsDictionaryBdc$new(resourceConnection)

Arguments

resourceConnection

A bdc::PicSureHpdsResourceConnectionBdc object.

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Method getKeyInfo()

Helper method to return key/path information from phenotype concept paths.

Usage

PicSureHpdsDictionaryBdc$getKeyInfo(key)

Arguments

key

The concept path key to look up.

Returns

Concept path information or FALSE.

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Method genotypeAnnotations()

Returns genotype annotations from info concept paths.

Usage

PicSureHpdsDictionaryBdc$genotypeAnnotations()

Returns

a data.frame object containing a table of genotype annotations.

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Method find()

This method returns a PicSureHpdsDictionaryBdcResult object containing the results of the search on the HPDS resource's data dictionary.

Usage

PicSureHpdsDictionaryBdc$find(term, limit = 0, offset = 0, showAll = FALSE)

Arguments

term

Term to find in the dictionary.

limit

Number of items to return.

offset

The offset record to start returning from.

showAll

Show all studies, not just ones within connection query scopes.

Returns

A bdc::PicSureHpdsDictionaryBdcResult object containing results from the dictionary.

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Method clone()

The objects of this class are cloneable with this method.

Usage

PicSureHpdsDictionaryBdc$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

hms-dbmi/pic-sure-biodatacatalyst-r-adapter-hpds documentation built on Sept. 24, 2022, 9:24 a.m.