Output

class alphagenome.models.v2.dna_output.Output(atac=None, cage=None, dnase=None, rna_seq=None, chip_histone=None, chip_tf=None, splice_sites=None, splice_site_usage=None, splice_junctions=None, contact_maps=None, sc_gene_expression=None, sc_atac=None, sc_gene_expression_denoised=None, cell_embeddings=None, methylation=None)

Model outputs for a single prediction.

atac

TrackData of type OutputType.ATAC.

cage

TrackData of type OutputType.CAGE.

dnase

TrackData of type OutputType.DNASE.

rna_seq

TrackData of type OutputType.RNA_SEQ.

chip_histone

TrackData of type OutputType.CHIP_HISTONE.

chip_tf

TrackData of type OutputType.CHIP_TF.

splice_sites

TrackData of type OutputType.SPLICE_SITES.

splice_site_usage

TrackData of type OutputType.SPLICE_SITE_USAGE.

splice_junctions

JunctionData of type OutputType.SPLICE_JUNCTIONS.

contact_maps

TrackData of type OutputType.CONTACT_MAPS.

sc_gene_expression

GeneExpressionData of type OutputType.SC_GENE_EXPRESSION.

sc_atac

TrackData of type OutputType.SC_ATAC.

sc_gene_expression_denoised

GeneExpressionData of type OutputType.SC_GENE_EXPRESSION_DENOISED (returned when requesting denoised expression with cell_conditioning=).

cell_embeddings

Numpy array of cell embeddings.

methylation

TrackData of type OutputType.METHYLATION.

Methods

filter_output_type(output_types)	Filters tracks to specific output type.
filter_to_observed()	Filters tracks to observed tracks across all populated outputs.
filter_to_strand(strand)	Filters tracks by DNA strand.
get(output_type)	Gets the track data for the specified output type.
map_over_outputs(fn)	Applies a transformation function to each TrackData or GeneExpressionData.
resize(width)	Resizes all tracks to a specified width.
with_metadata_column(name, value)	Returns a new Output with updated metadata column on all tracks.
with_name_suffix(suffix)	Returns a new Output object with suffixed track names on all tracks.