Using a Spark node/cluster on the UK Biobank Research Analysis Platform (DNAnexus), use R to extract a provided set of variables. Using code from the UK Biobank DNAnexus team https://github.com/UK-Biobank/UKB-RAP-Notebooks/blob/main/NBs_Prelim/105_export_participant_data_to_r.ipynb
Usage
get_rap_phenos(
names,
value_coding = "replace",
names_are_titles = FALSE,
record = NULL,
verbose = FALSE
)Arguments
- names
A string or vector of strings. The variable name(s) required. e.g., c("eid","p31","p21003_i0")
- value_coding
A string. How to handle coded fields. "replace" if a coding value exists, replace the raw value with the code; "raw" export the raw values of the field; "exclude" if a coding value exists, do not export the value (most commonly used with sparse fields).
default="replace"- names_are_titles
Logical. Passing DNAnexus variable "titles" e.g., c("Age at recruitment", "Standing height | Instance 0").
default=FALSE- record
A string. The `dnanexus_link` file descriptor of the .dataset to use. Default (if left as NULL) is to use the most recently dispensed dataset.
default=most recent dataset- verbose
Logical. Be verbose,
default=FALSE
Examples
# get phenotype data
ukb <- get_rap_phenos(c("eid","p31","p21003_i0","p53_i0"))
# save to file on the RAP worker node
readr::write_tsv(ukb, "ukbrap.phenos.20231114.txt.gz")
# upload data to RAP storage
upload_to_rap(file="ukbrap.phenos.20231114.txt.gz", dir="")