alphagenome_get_atac() — extract ATAC-seq predictions

alphagenome_get_atac() extracts ATAC-seq chromatin accessibility predictions from the list returned by alphagenome_query(). It accesses the atac slot of the underlying Python response object via reticulate::py_get_attr() and converts both the signal matrix and track metadata into native R objects. If "ATAC" was not included in requested_outputs, the function returns NULL.

Function signature

alphagenome_get_atac(response_body)

Parameters

response_body

list

required

The list returned by alphagenome_query(). Pass the return value of alphagenome_query() directly without modification.

Return value

result

list or NULL

Returns NULL if "ATAC" was not included in requested_outputs when calling alphagenome_query().Otherwise returns a named list with two elements:

Show list elements

values

numeric matrix

A numeric matrix with dimensions positions × tracks. Rows correspond to genomic positions; columns correspond to individual ATAC-seq signal tracks across tissues and cell types.

metadata

data.frame

A data frame with one row per track containing annotations such as tissue of origin, cell type, and other track-level metadata from the AlphaGenome API.

Example

library(AlphaGenomeR)

api_key <- Sys.getenv("ALPHAGENOME_API_KEY")

results <- alphagenome_query(
  access_token      = api_key,
  genomic_region    = "chr17:42560601-43609177",
  ontology_terms    = c("UBERON:0002048"),
  requested_outputs = c("ATAC")
)

atac_data <- alphagenome_get_atac(results)

dim(atac_data$values)    # positions x tracks matrix
head(atac_data$metadata) # track metadata

Include "ATAC" in requested_outputs when calling alphagenome_query(). The function returns NULL if "ATAC" was omitted, and accessing $values on NULL will produce an error.

Core Functions

Extractor Functions

alphagenome_get_atac() — extract ATAC-seq predictions

Function signature

Parameters

Return value

Example

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Core Functions

Extractor Functions

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