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AlphaGenomeR provides three extractor functions for splicing-related predictions: alphagenome_get_splice_sites() for per-position donor and acceptor site scores, alphagenome_get_splice_junctions() for predicted splice junction read counts, and alphagenome_get_splice_usage() for splice site usage rates. All three accept the list returned by alphagenome_query() and return NULL if the corresponding modality was not requested.

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alphagenome_get_splice_sites()

Splice site predictions score each genomic position in the queried interval for its likelihood of functioning as a donor (5′) or acceptor (3′) splice site. alphagenome_get_splice_sites() accesses the splice_sites slot of the Python response object.

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Function signature

alphagenome_get_splice_sites(response_body)

​
Parameters

​
response_body
list
required
The list returned by alphagenome_query(). Must have been called with "SPLICE_SITES" in requested_outputs.

​
Return value

​
result
list or NULL
Returns NULL if "SPLICE_SITES" was not in requested_outputs. Otherwise returns a named list:

​
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("SPLICE_SITES")
)

sites_data <- alphagenome_get_splice_sites(results)

dim(sites_data$values)    # positions x tracks
head(sites_data$metadata)

​
alphagenome_get_splice_junctions()

Splice junction predictions represent predicted read support for specific exon–exon junctions within the queried interval. alphagenome_get_splice_junctions() accesses the splice_junctions slot of the Python response object.

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Function signature

alphagenome_get_splice_junctions(response_body)

​
Parameters

​
response_body
list
required
The list returned by alphagenome_query(). Must have been called with "SPLICE_JUNCTIONS" in requested_outputs.

​
Return value

​
result
list or NULL
Returns NULL if "SPLICE_JUNCTIONS" was not in requested_outputs. Otherwise returns a named list:

​
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("SPLICE_JUNCTIONS")
)

junctions_data <- alphagenome_get_splice_junctions(results)

dim(junctions_data$values)    # positions x tracks
head(junctions_data$metadata)

​
alphagenome_get_splice_usage()

Splice site usage predictions capture the fraction of transcripts that use each splice site, providing a view of alternative splicing regulation. alphagenome_get_splice_usage() accesses the splice_site_usage slot (note the internal Python attribute name) of the response object.

​
Function signature

alphagenome_get_splice_usage(response_body)

​
Parameters

​
response_body
list
required
The list returned by alphagenome_query(). Splice site usage data is returned when splicing outputs are requested (e.g., "SPLICE_SITES" or "SPLICE_JUNCTIONS"). The function reads the splice_site_usage attribute from the Python response object directly.

​
Return value

​
result
list or NULL
Returns NULL if splice site usage data is not present in the response. Otherwise returns a named list:

​
Example

library(AlphaGenomeR)

api_key <- Sys.getenv("ALPHAGENOME_API_KEY")

# Request splicing outputs; splice_site_usage is populated alongside them
results <- alphagenome_query(
  access_token      = api_key,
  genomic_region    = "chr17:42560601-43609177",
  ontology_terms    = c("UBERON:0002048"),
  requested_outputs = c("SPLICE_SITES", "SPLICE_JUNCTIONS")
)

usage_data <- alphagenome_get_splice_usage(results)

if (!is.null(usage_data)) {
  dim(usage_data$values)    # positions x tracks
  head(usage_data$metadata)
}
alphagenome_get_splice_usage() reads the splice_site_usage attribute from the Python response object directly. It does not require a dedicated requested_outputs token — splice usage data is available when splicing outputs are requested. The function returns NULL if the attribute is absent from the response.

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