Class: Google::Apis::GenomicsV1::VariantAnnotation

Inherits:
Object
  • Object
show all
Includes:
Core::Hashable, Core::JsonObjectSupport
Defined in:
generated/google/apis/genomics_v1/classes.rb,
generated/google/apis/genomics_v1/representations.rb,
generated/google/apis/genomics_v1/representations.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from Core::JsonObjectSupport

#to_json

Methods included from Core::Hashable

process_value, #to_h

Constructor Details

#initialize(**args) ⇒ VariantAnnotation

Returns a new instance of VariantAnnotation



3585
3586
3587
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 3585

def initialize(**args)
   update!(**args)
end

Instance Attribute Details

#alternate_bases ⇒ String

The alternate allele for this variant. If multiple alternate alleles exist at this location, create a separate variant for each one, as they may represent distinct conditions. Corresponds to the JSON property alternateBases

Returns:

  • (String) 


3547
3548
3549
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 3547

def alternate_bases
  @alternate_bases
end

#clinical_significance ⇒ String

Describes the clinical significance of a variant. It is adapted from the ClinVar controlled vocabulary for clinical significance described at: http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/ Corresponds to the JSON property clinicalSignificance

Returns:

  • (String) 


3555
3556
3557
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 3555

def clinical_significance
  @clinical_significance
end

#conditions ⇒ Array<Google::Apis::GenomicsV1::ClinicalCondition>

The set of conditions associated with this variant. A condition describes the way a variant influences human health. Corresponds to the JSON property conditions

Returns:



3561
3562
3563
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 3561

def conditions
  @conditions
end

#effect ⇒ String

Effect of the variant on the coding sequence. Corresponds to the JSON property effect

Returns:

  • (String) 


3566
3567
3568
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 3566

def effect
  @effect
end

#gene_id ⇒ String

Google annotation ID of the gene affected by this variant. This should be provided when the variant is created. Corresponds to the JSON property geneId

Returns:

  • (String) 


3572
3573
3574
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 3572

def gene_id
  @gene_id
end

#transcript_ids ⇒ Array<String>

Google annotation IDs of the transcripts affected by this variant. These should be provided when the variant is created. Corresponds to the JSON property transcriptIds

Returns:

  • (Array<String>) 


3578
3579
3580
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 3578

def transcript_ids
  @transcript_ids
end

#type ⇒ String

Type has been adapted from ClinVar's list of variant types. Corresponds to the JSON property type

Returns:

  • (String) 


3583
3584
3585
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 3583

def type
  @type
end

Instance Method Details

#update!(**args) ⇒ Object

Update properties of this object



3590
3591
3592
3593
3594
3595
3596
3597
3598
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 3590

def update!(**args)
  @alternate_bases = args[:alternate_bases] if args.key?(:alternate_bases)
  @clinical_significance = args[:clinical_significance] if args.key?(:clinical_significance)
  @conditions = args[:conditions] if args.key?(:conditions)
  @effect = args[:effect] if args.key?(:effect)
  @gene_id = args[:gene_id] if args.key?(:gene_id)
  @transcript_ids = args[:transcript_ids] if args.key?(:transcript_ids)
  @type = args[:type] if args.key?(:type)
end