Package index • ofhelper

All functions

clean_codings_table(): Clean OFH Codings Table
clean_data_dictionary(): Clean OFH Data Dictionary
collapse_cmd_args(): Collapse Command Arguments
correct_column_type(): Correct Data Column Type
create_bgen_annotation(): Create BGEN File Annotation
create_bgen_file_names(): Create OFH genomic file BGEN file names
create_cmd_input_string(): Create Command Input String for Jupyter Workstation
create_genomic_file_batch_ids(): Create batch ID string for genomic files
create_genomic_file_prefix(): Create genomic file prefix
create_imputed_file_prefix(): Create OFH imputed genomic file prefix
create_ofhelper_string(): Create Complete ofhelper Package Source String
create_sample_file_names(): Create OFH imputed genomic file BGEN Sample file names
create_snv_file_prefix(): Create OFH called genotype file prefix
decode_multi_select(): Decode Multi-Select Variables
decode_ofh_variable(): Decode OFH Variable
decode_raw_ofh_file(): Decode Raw OFH Data File
decode_single_select(): Decode Single-Select Variables
decompress_gzip(): Decompress gzipped files
dx_auth(): Authenticate with DNAnexus
dx_check(): Check DNAnexus Environment Status
dx_check_auth(): Check DNAnexus Authentication
dx_check_binary(): Check DNAnexus Binary
dx_check_connection(): Check DNAnexus API Connectivity
dx_check_path(): Check DNAnexus Path
dx_check_project(): Check DNAnexus Project
dx_clear_env(): Clear DNAnexus Environment
dx_download(): Download Files from DNAnexus
dx_file_exists(): Check if a File Exists on DNAnexus
dx_find_projects(): Find DNAnexus Projects
dx_get_env(): Get DNAnexus Environment Information
dx_get_path(): Get the DNAnexus path
dx_get_project(): Get the DNAnexus project ID
dx_init(): Initialize DNAnexus Environment
dx_is_initialized(): Check if DNAnexus is Initialized
dx_launch_workstation(): Launch a DNAnexus Workstation Session
dx_ls(): List Contents of DNAnexus Directory
dx_remount_project(): Remount DNAnexus Project
dx_run_cmd(): Run Arbitrary DX Commands
dx_run_swiss_army_knife(): Submit a Swiss Army Knife DNAnexus Job
dx_set_binary(): Set DNAnexus Binary Path
dx_set_env(): Set DNAnexus Environment Cache
dx_set_path(): Set DNAnexus Path
dx_set_project(): Set DNAnexus Project
dx_submit_r_job(): Submit R Script as DNAnexus Job
dx_upload(): Upload Files to DNAnexus
explode_multi_select(): Explode Multi-Select Variables into Dummy Codes
export_entities(): Export Entities from DNAnexus
find_tre_instance_type(): Find Suitable DNAnexus Instance Type
get_dx_cache(): Get values from the DNAnexus cache
get_workstation_worker_url(): Get Workstation Worker URL
init_dx_cache(): Initialize the DNAnexus cache environment
rate_card: Our Future Health TRE rate card
remove_dx_cache(): Remove all entries from the DNAnexus cache
reset_dx_cache(): Reset the DNAnexus cache
set_dx_cache(): Set values in the DNAnexus cache
tre_path(): Create TRE-compatible path
tre_rate_card(): Get TRE Rate Card