interface to a small subset of UKBB summary stats in MatrixTable format

Usage

get_ukbb_sumstat_10kloci_mt(
  hl,
  folder = tempdir(),
  cache = BiocFileCache::BiocFileCache(),
  timeout.ukbb = 3600,
  simple = FALSE
)

Arguments

hl: hail object
folder: character(1) destination of 1kg.mt as retrieved using hl.utils.get_1kg, import_vcf, write
cache: a BiocFileCache-type cache
timeout.ukbb: numeric(1) defaults to 3600 for timeout setting in `options()`; option value is reset on exit
simple: logical(1) avoids basilisk if TRUE

Value

"hail.matrixtable.MatrixTable" instance

Note

The loci were selected using a .000345 of over 28 million loci recorded in the UKBB pan-ancestry record. The sample is made available a) to assess some issues with data volume (the full resource is about 12.78 TB according to [this doc](https://pan-dev.ukbb.broadinstitute.org/docs/hail-format/index.html), and b) to provide full information on the scope of phenotypes and populations available.

This function will unzip 5GB of MatrixTable data. It may be desirable to cache the unzipped image to a persistent location. If this has been done and the environment variable `HAIL_UKBB_SUMSTAT_10K_PATH` has been set to this location, this function will use the MatrixTable content found there.

Examples

hl <- hail_init()
ss <- get_ukbb_sumstat_10kloci_mt(hl)
# consider saving the unzipped image and recaching
ss$count()
#> [[1]]
#> [1] 9888
#> 
#> [[2]]
#> [1] 7271
#>