Class: Google::Apis::GenomicsV1beta2::VariantAnnotation

Inherits:
Object
  • Object
show all
Includes:
Core::Hashable
Defined in:
generated/google/apis/genomics_v1beta2/classes.rb,
generated/google/apis/genomics_v1beta2/representations.rb,
generated/google/apis/genomics_v1beta2/representations.rb

Overview

A Variant annotation.

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from Core::Hashable

process_value, #to_h

Constructor Details

#initialize(**args) ⇒ VariantAnnotation

Returns a new instance of VariantAnnotation.



3194
3195
3196
 
# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 3194

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) 


3157
3158
3159
 
# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 3157

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) 


3164
3165
3166
 
# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 3164

def clinical_significance
  @clinical_significance
end

#conditions ⇒ Array<Google::Apis::GenomicsV1beta2::VariantAnnotationCondition>

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:



3170
3171
3172
 
# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 3170

def conditions
  @conditions
end

#effect ⇒ String

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

Returns:

  • (String) 


3175
3176
3177
 
# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 3175

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) 


3181
3182
3183
 
# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 3181

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>) 


3187
3188
3189
 
# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 3187

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) 


3192
3193
3194
 
# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 3192

def type
  @type
end

Instance Method Details

#update!(**args) ⇒ Object

Update properties of this object



3199
3200
3201
3202
3203
3204
3205
3206
3207
 
# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 3199

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