validate: Validate RCX and its aspects

In frankkramer-lab/RCX: R package implementing the Cytoscape Exchange (CX) format

Validate RCX and its aspects

Description

Validate RCX objects and its aspects.

Usage

validate(x, verbose = TRUE)

## Default S3 method:
validate(x, verbose = TRUE)

## S3 method for class 'NodesAspect'
validate(x, verbose = TRUE)

## S3 method for class 'EdgesAspect'
validate(x, verbose = TRUE)

## S3 method for class 'NodeAttributesAspect'
validate(x, verbose = TRUE)

## S3 method for class 'EdgeAttributesAspect'
validate(x, verbose = TRUE)

## S3 method for class 'NetworkAttributesAspect'
validate(x, verbose = TRUE)

## S3 method for class 'CartesianLayoutAspect'
validate(x, verbose = TRUE)

## S3 method for class 'CyGroupsAspect'
validate(x, verbose = TRUE)

## S3 method for class 'CyVisualPropertiesAspect'
validate(x, verbose = TRUE)

## S3 method for class 'CyVisualProperty'
validate(x, verbose = TRUE)

## S3 method for class 'CyVisualPropertyProperties'
validate(x, verbose = TRUE)

## S3 method for class 'CyVisualPropertyDependencies'
validate(x, verbose = TRUE)

## S3 method for class 'CyVisualPropertyMappings'
validate(x, verbose = TRUE)

## S3 method for class 'CyHiddenAttributesAspect'
validate(x, verbose = TRUE)

## S3 method for class 'CyNetworkRelationsAspect'
validate(x, verbose = TRUE)

## S3 method for class 'CySubNetworksAspect'
validate(x, verbose = TRUE)

## S3 method for class 'CyTableColumnAspect'
validate(x, verbose = TRUE)

## S3 method for class 'RCX'
validate(x, verbose = TRUE)

Arguments

x	object to validate; RCX object or an aspect
verbose	logical; whether to print the test results.

Details

Different tests are performed on aspects and the RCX network. This includes checks of the correct aspect structure, data types, uniqueness of IDs and attribute names, presence of NA values, and references between the aspects.

Value

logical; whether the object passed all tests.

Methods (by class)

• default: Default

• NodesAspect: Nodes

• EdgesAspect: Edges

• NodeAttributesAspect: Node attributes

• EdgeAttributesAspect: Edge attributes

• NetworkAttributesAspect: Network attributes

• CartesianLayoutAspect: Cartesian layout

• CyGroupsAspect: Cytoscape Groups

• CyVisualPropertiesAspect: Cytoscape Visual Properties

• CyVisualProperty: Cytoscape Visual Properties

• CyVisualPropertyProperties: Cytoscape visual property: Properties

• CyVisualPropertyDependencies: Cytoscape visual property: Dependencies

• CyVisualPropertyMappings: Cytoscape visual property: Mappings

• CyHiddenAttributesAspect: Cytoscape hidden attributes

• CyNetworkRelationsAspect: Cytoscape network relations

• CySubNetworksAspect: Cytoscape sub-networks

• CyTableColumnAspect: Cytoscape table column aspect

• RCX: The whole RCX object with all its aspects

Examples

## Read from a CX file
## reading the provided example network of the package
cxFile <- system.file(
 "extdata", 
 "Imatinib-Inhibition-of-BCR-ABL-66a902f5-2022-11e9-bb6a-0ac135e8bacf.cx", 
 package = "RCX"
)

rcx = readCX(cxFile)

## validate the network
validate(rcx)

## validate a single aspect
validate(rcx$nodes)

frankkramer-lab/RCX documentation built on Feb. 4, 2023, 5:12 p.m.