Table 2 Additional RGMQL functions to handle initialization, remote data exploration, processing and result conversions

FUNCTIONS TO HANDLE, READ AND ANALYZE LOCAL AND REMOTE DATASETS, PROVINDING ALSO USEFUL CONVERSIONS

delete_dataset()

It deletes a private dataset from remote repository

Remote dataset

–

YES

download_dataset()

It downloads a private dataset from remote repository to local path

Remote dataset

Local dataset

YES

download_as_GRangesList()

It downloads a private dataset into R environment as a GRangesList

Remote dataset

GRangesList

YES

export_gmql()

It creates a GDM-like dataset from a GRangesList

GRangesList

Local dataset

NO

filter_and_extract()

It filters based on metadata predicates and generates a new GRanges with a chosen list of region attributes. It works if samples have their region coordinates (chr, ranges, strand) in the same order

Local dataset/ GRangesList

GRanges

NO

import_gmql()

It creates a GRangesList from a GDM-like dataset

Local dataset

GRangesList

NO

read_gmql()

It reads a GMQLDataset from a dataset (with a valid format) on disk, or from the remoterepository in case of remote processing

Local/Remote dataset

GMQLDataset

YES, if is_local = FALSE

read_GRangesList()

It reads a GMQLDataset from a GRangeList

GRangesList

GMQLDataset

NO

sample_metadata()

It retrieves metadata of a specific sample in a dataset

Remote dataset

–

YES

sample_region()

It retrieves regions data of a specific sample in a dataset

Remote dataset

–

YES

semijoin()

It supports the filter method defining semijoin conditions on metadata

–

–

NO

show_datasets_list()

It shows all GMQL datasets in remote repository, both public or privately stored by the user

–

–

YES

show_all_metadata()

It shows all metadata of a given GMQL dataset either locally or in the remote repository

–

–

NO

show_samples_list()

It show all samples of a GMQL dataset on the remote repository

–

–

YES

show_schema()

It shows the region attribute schema of a GMQL dataset on the remote repository

–

–

YES

take()

It saves as a GRangesList any dataset resulting from local processing. If invoked after collect(), the dataset is materialized also in local File System

GMQLDataset

GRangesList

NO, only for local processing

upload_dataset()

It uploads a dataset (GDM or not), and a corresponding GMQL dataset is created on the remote repository

Local dataset

Remote dataset

YES

FUNCTIONS TO HANDLE GMQL SERVER AND MONITOR REMOTE JOBS, IF NEEDED

init_gmql()

It initializes and runs GMQL server to execute any processing, and also performs a login to GMQL REST services suite, if needed

–

–

NO

login_gmql()

Login to GMQL REST services suite as a registered user, specifying username and password, or as guest

–

–

YES

logout_gmql()

Logout from GMQL REST services suite

–

–

YES

register_gmql()

Register to GMQL REST services suite

–

–

YES

remote_processing()

It allows to enable or disable remote processing

–

–

YES

show_jobs_log()

It shows the log of a specific job

–

–

YES

trace_job()

It traces a specific job

–

–

YES

show_job_list()

It shows all jobs (run, succeded or failed) invoked by the user on the remote GMQL server

–

–

YES

show_queries_list()

It shows all the GMQL queries saved by the user on the remote repository

–

–

YES

stop_gmql()

It stops the GMQL server processing

–

–

NO

stop_job()

It stops a specific job

–

–

YES

FUNCTIONS USING QUERIES IN GMQL SYNTAX

compile_query()

It compiles a GMQL query inserted as a text string

–

–

YES

compile_query_fromfile()

It compiles a GMQL query taken from a file

–

–

YES

run_query()

It runs a GMQL query inserted as a text string

–

–

YES

run_query_fromfile()

It runs a GMQL query taken from a file

–

–

YES

save_query()

It saves into the remote repository a GMQL query, taken from a file

–

–

YES

save_query_fromfile()

It saves into the remote repository a GMQL query, inserted as a text string

–

–

YES