Function to read the UK Biobank BGEN files into a bigSNP.

snp_readBGEN(
bgenfiles,
backingfile,
list_snp_id,
ind_row = NULL,
bgi_dir = dirname(bgenfiles),
ncores = 1
)

## Arguments

bgenfiles Character vector of paths to files with extension ".bgen". The corresponding ".bgen.bgi" index files must exist. The path (without extension) for the backing files for the cache of the bigSNP object. List (same length as the number of BGEN files) of character vector of SNP IDs to read. These should be in the form "___" (e.g. "1_88169_C_T" or "01_88169_C_T"). This function assumes that these IDs are uniquely identifying variants. An optional vector of the row indices (individuals) that are used. If not specified, all rows are used. Don't use negative indices. Directory of index files. Default is the same as bgenfiles. How to read BGEN probabilities? Currently implemented: as dosages (rounded to two decimal places), the default, as hard calls, randomly sampled based on those probabilities (similar to PLINK option '--hard-call-threshold random'). Number of cores used. Default doesn't use parallelism. You may use nb_cores().

## Value

The path to the RDS file that stores the bigSNP object. Note that this function creates one other file which stores the values of the Filebacked Big Matrix.
You shouldn't read from BGEN files more than once. Instead, use snp_attach to load the "bigSNP" object in any R session from backing files.

## Details

This function is designed to read UK Biobank imputation files. This assumes that variants have been compressed with zlib, that there are only 2 possible alleles, and that each probability is stored on 8 bits. For example, if you use qctool to generate your own BGEN files, please make sure you are using options '-ofiletype bgen_v1.2 -bgen-bits 8'.
If the format is not the expected one, this will result in an error or even a crash of your R session. Another common source of error is due to corrupted files; e.g. if using UK Biobank files, compare the result of tools::md5sum() with the ones at https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=998.