In the UK Biobank RAP export tables for HES, GP, death, and cancer registry data, plus self-reported illness fields, using the table-exporter. This is essentially a wrapper function to submit jobs to the table exporter.
Suggest executing in an RStudio session. ~10Gb of text files are created. This will cost ~£0.15 per month to store in the RAP standard storage.
Usage
export_tables(
submit = FALSE,
ignore_warnings = FALSE,
file_paths = ukbrapR:::ukbrapr_paths,
dataset = NULL,
verbose = FALSE
)Arguments
- submit
Logical. Actually submit `dx` commands. Default is FALSE i.e., just check inputs & file paths, then print the commands,
default=FALSE- ignore_warnings
Logical. If an exported table already exists do not submit the table-exporter command unless this is TRUE,
default=FALSE- file_paths
A data frame. Columns must be `object` and `path` containing paths to outputted files. If blank, will use the default paths,
default=ukbrapR:::ukbrapr_paths- dataset
A string. If you wish to specify dataset. If blank, will use the most recently dispensed dataset in the main project directory.
default=app#####_#####.dataset- verbose
Logical. Be verbose,
default=FALSE
Examples
# To keep files organised this package assumes the following file structure
# This object is not actually required but illstrates the defaults to be
# created in your RAP space (override by providing a new `file_paths`):
ukbrapr_paths = data.frame(
object=c("death","death_cause","hesin","hesin_diag","hesin_oper","gp_clinical","gp_scripts","selfrep_illness","cancer_registry","baseline_dates"),
path=c(
"ukbrapr_data/death.tsv",
"ukbrapr_data/death_cause.tsv",
"ukbrapr_data/hesin.tsv",
"ukbrapr_data/hesin_diag.tsv",
"ukbrapr_data/hesin_oper.tsv",
"ukbrapr_data/gp_clinical.tsv",
"ukbrapr_data/gp_scripts.tsv",
"ukbrapr_data/selfrep_illness.tsv",
"ukbrapr_data/cancer_registry.tsv",
"ukbrapr_data/baseline_dates.tsv"
)
)
ukbrapr_paths
# test run to see `dx run table-exporter` commands - but will not submit jobs
export_tables()
# Submit all `dx run table-exporter` commands. ~10Gb of text files are created. This will cost ~£0.15 per month to store in the RAP standard storage.
export_tables(submit=TRUE)