Package index • ukbrapR

Export required data

export_tables(): Export diagnosis files to RAP persistent storage

Extract genetic variants

extract_variants(): Extract variants from bulk data and load to memory

make_imputed_bed(): Extract variants from imputed genotype file(s) into single BED file

make_dragen_bed(): Extract variants from DRAGEN BGEN file(s) into single BED file

load_bed(): Load BED file into memory

Create polygenic score

create_pgs(): Create a polygenic score

Ascertain diagnoses and determine date first diagnosed

get_diagnoses(): Get UK Biobank participant diagnosis data

get_df(): Get UK Biobank participant Date First (DF) diagnosis

Working with UK Biobank data fields

fields_to_phenos(): Check UK Biobank field IDs

label_ukb_fields(): Update a data frame containing UK Biobank fields with `title` and `label` from the schema

label_ukb_field(): Update UK Biobank field with `title` and `label` from the schema

Upload/download from RAP/worker storage

upload_to_rap(): Use R to upload a file to the UK Biobank RAP

download_from_rap(): Use R to download a file to the UK Biobank RAP

Spark

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

get_emr_spark(): Get UK Biobank participant Electronic Medical Records (EMR) data in a RAP Spark environment