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), read_as = c("dosage", "random"), ncores = 1 )
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
An optional vector of the row indices (individuals) that
are used. If not specified, all rows are used.
Directory of index files. Default is the same as
How to read BGEN probabilities? Currently implemented:
Number of cores used. Default doesn't use parallelism.
You may use
The path to the RDS file that stores the
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.
For more information on this format, please visit BGEN webpage.
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.
# See e.g. https://github.com/privefl/UKBiobank/blob/master/10-get-dosages.R