Submit Clue queries — clue_query_submit • cluequery

Submit query gene sets in GMT format as jobs to Clue.

Usage

clue_query_submit(up_gmt, down_gmt, name = NULL, api_key = NULL)

clue_queries_submit(queries, api_key = NULL, interval = 60)

Arguments

up_gmt, down_gmt: Path to GMT files containing the lists of up- and down-regulated genes.
name: Name for job.
api_key: Clue API key. Leave empty if it is saved in ~/.Renviron.
queries: Named list of lists, each with an up and down slot containing up- and down-regulated GMT files. Job names are derived from the list names.
interval: Check every x seconds.

Value

Nested list of job parameters returned by Clue.

Details

GMT files can be generated using the clue_prepare_funs functions or write_gmt.

Functions

clue_queries_submit: Submit multiple queries to Clue