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alphagenome_get_rna_seq() extracts RNA-seq gene expression predictions from the list returned by alphagenome_query(). It uses reticulate::py_get_attr() to access the rna_seq slot of the Python response object and converts both the numeric values array and the track metadata data frame into native R objects. If "RNA_SEQ" was not included in requested_outputs, the function returns NULL.

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Function signature

alphagenome_get_rna_seq(response_body)

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Parameters

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response_body
list
required
The list returned by alphagenome_query(). This object wraps the converted Python prediction response. Pass the return value of alphagenome_query() directly without modification.

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Return value

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

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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("RNA_SEQ")
)

rna_data <- alphagenome_get_rna_seq(results)

dim(rna_data$values)    # positions x tracks matrix
head(rna_data$metadata) # track metadata
alphagenome_get_rna_seq() returns NULL if "RNA_SEQ" was not listed in requested_outputs. Always check the return value before accessing $values or $metadata.

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