Corrected functionality:
Updated earlier typo/change that made ukb_df incorrectly
convert all column types to character (caused by replacing
stringr::str_interp to stringr::str_c when
passing internal column type vector to data.table::fread,
without updating argument)
Bug fix:
Cleared bug in ukb_icd_freq_by for disease frequency
against a quantitative trait.
Made ukb_df column name from description regex
find/replace more general to capture all variations of “uses data
coding”
Updated functionality:
ukb_icd_keyword internal regex search
ignore.case defaults to TRUE, with and option
to set added to arguments.
Test data:
Added example UKB data ukbXXXX.tab, ukbXXXX.r, ukbXXXX.html to test
the ‘read’ and ‘summarise’ functionality ukb_df,
ukb_df_field, and ukb_context. See the section
“An example fileset” in the vignette for details.
Updated functionality:
ukb_icd_freq_by with freq.plot = TRUE plots
a barplot for categorical reference variables, and plots diagnosis
frequencies at the midpoint of each group for quantitative reference
variables.
Webpage:
The ukbtools webpage has been rebuilt with pkgdown and includes the vignette under the Articles tab.
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:
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:
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).Bug fix:
ukb_icd_freq_by: corrected order by levels of
reference.var in the optional plot. (order in the default
dataframe returned was correct.)
ukb_df: corrected tab file path update in r source
file. Specifically, made regular expression more specific (1 case
reported of regular expression matching word elsewhere in the source
file.). Also, replaced utils::read.delim with readr::read_tsv for faster
read, with progress bar.
New functionality:
ukb_icd_freq_by returns frequency for one or more
ICD diagnoses by levels of a reference variable and includes an optional
plot
ukb_df_full_join (a thin wrapper around
dplyr::full_join) recursively called on a list of UKB
datasets
ukb_df_duplicated_names to identify duplicated names
within a dataset. The variable prefix (constructed from its
description), index, and array should make the column name unique.
However, typos in UKB documentation that give two variables the do not
increment index/array have been observed. You will want to identify
these and update them appropriately. We expect the occurrence of such
duplicates will be rare.
Updated functionality:
ukb_icd_diagnosis now takes one or more individual
ids and returns a dataframe with a potential message noting ids with no
diagnoses
ukb_icd_keyword accepts a character vector of one or
more “keywords” and returns all ICD descriptions including any of the
keywords