# R functions to use in the UK Biobank Research Analysis Platform (RAP)

## Documentation for package ‘ukbrapR’ version 0.3.4

- DESCRIPTION file.
- Package NEWS.

## Help Pages

create_pgs | Create a polygenic score
download_from_rap | Use R to download a file to the UK Biobank RAP
export_tables | Export diagnosis files to RAP persistent storage
extract_variants | Extract variants from bulk data and load to memory
fields_to_phenos | Check UK Biobank field IDs
get_df | Get UK Biobank participant Date First (DF) diagnosis
get_diagnoses | Get UK Biobank participant diagnosis data
get_emr_spark | Get UK Biobank participant Electronic Medical Records (EMR) data in a RAP Spark environment
get_rap_phenos | Get UK Biobank participant phenotype data
get_selfrep_illness_spark | Get UK Biobank participant self-reported illness/year data for specific codes
label_ukb_field | Update UK Biobank field with 'title' and 'label' from the schema
label_ukb_fields | Update a data frame containing UK Biobank fields with 'title' and 'label' from the schema
load_bed | Load BED file into memory
make_dragen_bed | Extract variants from DRAGEN PGEN file(s) into single BED file
make_dragen_bed_from_pvcfs | Extract variants from DRAGEN pVCF file(s) into single BED file
make_imputed_bed | Extract variants from imputed genotype file(s) into single BED file
upload_to_rap | Use R to upload a file to the UK Biobank RAP