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Sends a query to the Synthesize Bio API for prediction and retrieves gene expression samples. This function sends the query to the API and processes the response into usable data frames.

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Usage

predict_query(
  query,
  model_id,
  api_base_url = API_BASE_URL,
  poll_interval_seconds = DEFAULT_POLL_INTERVAL_SECONDS,
  poll_timeout_seconds = DEFAULT_POLL_TIMEOUT_SECONDS,
  return_download_url = FALSE,
  raw_response = FALSE,
  ...
)

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Arguments

  • query: A list representing the query data to send to the API. Use get_example_query() to generate an example. The query supports additional optional fields: total_count (integer): Library size used when converting predicted log CPM back to raw counts. Higher values scale counts up proportionally. deterministic_latents (logical): If TRUE, the model uses the mean of each latent distribution instead of sampling, producing deterministic outputs for the same inputs. Useful for reproducibility. seed (integer): Random seed for reproducibility.
  • model_id: Character string specifying the model ID (e.g., “gem-1-bulk”, “gem-1-sc”). Use list_models() to see available models.
  • api_base_url: The base URL for the API server. Default is API_BASE_URL.
  • poll_interval_seconds: Seconds between polling attempts of the status endpoint. Default is DEFAULT_POLL_INTERVAL_SECONDS (2).
  • poll_timeout_seconds: Maximum total seconds to wait before timing out. Default is DEFAULT_POLL_TIMEOUT_SECONDS (900 = 15 minutes).
  • return_download_url: Logical, if TRUE, returns a list containing the signed download URL instead of parsing into data frames. Default is FALSE.
  • raw_response: Logical, if TRUE, returns the raw (unformatted) JSON response from the API without applying any output transformers. Default is FALSE.
  • ...: Additional parameters to include in the query body. These are passed directly to the API and validated server-side.

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Returns

A list. If return_download_url is FALSE (default), the list contains two data frames: metadata and expression. If TRUE, the list contains download_url and empty metadata and expression data frames.

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Examples

# Set your API key (in practice, use a more secure method)
# To start using rsynthbio, first you need to have an account with synthesize.bio.
# Go here to create one: https://app.synthesize.bio/

set_synthesize_token()

# Get available models
models <- list_models()

# Create a query for a specific model
query <- get_example_query(model_id = "gem-1-bulk")$example_query

# Request raw counts
result <- predict_query(query, model_id = "gem-1-bulk")

# Access the results
metadata <- result$metadata
expression <- result$expression

# Explore the top expressed genes in the first sample
head(sort(expression[1, ], decreasing = TRUE))

# Use deterministic latents for reproducible results
query$deterministic_latents <- TRUE
result_det <- predict_query(query, model_id = "gem-1-bulk")

# Specify a custom total count (library size)
query$total_count <- 5000000
result_custom <- predict_query(query, model_id = "gem-1-bulk")

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Source

Generated from R/call_model_api.R and the package help files in man/.