Skip to main content

Documentation Index

Fetch the complete documentation index at: https://mintlify.com/BDB-Genomics/AlphaGenomeR/llms.txt

Use this file to discover all available pages before exploring further.

Three extractor functions cover transcription-related signal modalities: alphagenome_get_cage() for CAGE-seq transcription start site signal, alphagenome_get_dnase() for DNase-seq chromatin accessibility, and alphagenome_get_procap() for PRO-cap nascent transcription signal. All three follow the same interface — they accept the list returned by alphagenome_query() and return a named list with $values and $metadata, or NULL if the corresponding modality was not requested.

​
CAGE

Cap Analysis of Gene Expression (CAGE) measures transcription start site (TSS) activity at single-nucleotide resolution. alphagenome_get_cage() extracts the cage slot from the AlphaGenome response.

​
Function signature

alphagenome_get_cage(response_body)

​
Parameters

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

​
Return value

​
result
list or NULL
Returns NULL if "CAGE" 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("CAGE")
)

cage_data <- alphagenome_get_cage(results)

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

​
DNase

DNase-seq measures genome-wide chromatin accessibility by identifying sites hypersensitive to DNase I cleavage. alphagenome_get_dnase() extracts the dnase slot from the AlphaGenome response.

​
Function signature

alphagenome_get_dnase(response_body)

​
Parameters

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

​
Return value

​
result
list or NULL
Returns NULL if "DNASE" 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("DNASE")
)

dnase_data <- alphagenome_get_dnase(results)

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

​
PRO-cap

PRO-cap (Precision Run-On and Capping) measures the density of RNA polymerases paused near transcription start sites, providing a direct readout of nascent transcription initiation. alphagenome_get_procap() extracts the procap slot from the AlphaGenome response.

​
Function signature

alphagenome_get_procap(response_body)

​
Parameters

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

​
Return value

​
result
list or NULL
Returns NULL if "PROCAP" 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("PROCAP")
)

procap_data <- alphagenome_get_procap(results)

dim(procap_data$values)    # positions x tracks
head(procap_data$metadata)
Each extractor returns NULL if its corresponding modality was not included in requested_outputs. You can request multiple modalities in a single call: requested_outputs = c("CAGE", "DNASE", "PROCAP").

Build docs developers (and LLMs) love

Get started for freeTalk to us