clue_query_submit: Submit Clue queries

In labsyspharm/cluequery: Query the Clue Database of Perturbations Using R

Submit Clue queries

Description

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.

Details

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

Value

Nested list of job parameters returned by Clue.

Functions

• clue_queries_submit: Submit multiple queries to Clue

labsyspharm/cluequery documentation built on May 23, 2022, 6:25 a.m.