Skip to content

ukbtools v0.11.0

Choose a tag to compare

View all tags
@kenhanscombe kenhanscombe released this 24 May 09:50
· 87 commits to master since this release
v0.11.0
8eac69a

Updated functionality:

  • ukb_df: Replaced readr::read_tsv with data.table::fread for faster read. Also includes an n_threads argument passed to data.table::fread, which may make read faster. Column names now include field code to ensure names are unique (UK Biobank sometimes use the same description for more than one variable)

Defunct functionality:

  • Added defunct message to ukb_gen_meta, ukb_gen_pcs, ukb_gen_excl, ukb_gen_rel, ukb_gen_het, ukb_gen_excl_to_na, and ukb_gen_write_plink_excl. ukb_defunct explains why these have become defunct and where to get UK Biobank genetic (meta)data.

New functionality:

  • Since the UKB changed the way they serve up genetic metadata, the following work with files described in UKB Resource 531: ukb_gen_sqc_names supplies column names for the separately downloaded sample QC file; ukb_gen_rel_count does the same as before (a count of levels of relatedness or a plot) but with separately downloaded relatedness data; ukb_gen_related_with_data returns subset of relatedness data in which both IDs have data on a phenotype of interest; ukb_gen_samples_to_remove returns a list of individuals to exclude in order to remove relatedness (one possible solution to a maximal subset problem).
Assets 2
Loading