MethylationScorer

class alphagenome.models.v2.variant_scorers.MethylationScorer(width)

Variant scorer for CpG methylation.

Variant scorer that quantifies a variant’s impact on CpG methylation. Scores are reported per CpG site found in the reference sequence within a window centered on the variant. Rows of the returned data are CpG positions.

Only CpG sites present in both the REF and ALT sequences are scored. Sites created or destroyed by the variant are omitted, since no ALT-versus-REF difference is defined for them.

width

The full width of the window around the variant within which CpG sites are scored, i.e. 2 * radius + 1.

requested_output

The requested output type (always METHYLATION).

base_variant_scorer

The base variant scorer.

name

The name of the scorer (a composite of the above attributes that uniquely identifies a scorer combination).

is_signed

Whether this variant scorer is directional (such that scores may be negative or positive) or non-directional (scores are always non-negative).

to_proto()

Converts the scorer to its corresponding proto message.

Raises:

ValueError – If the width is not supported.