BGEN matrix product
Compute a matrix product between BGEN files and a matrix. This removes the
need to read an intermediate FBM object with snp_readBGEN() to compute the
product. Moreover, when using dosages, they are not rounded to two decimal
places anymore.
snp_prodBGEN(
bgenfiles,
beta,
list_snp_id,
ind_row = NULL,
bgi_dir = dirname(bgenfiles),
read_as = c("dosage", "random"),
block_size = 1000,
ncores = 1
)bgenfiles |
Character vector of paths to files with extension ".bgen". The corresponding ".bgen.bgi" index files must exist. |
beta |
A matrix (or a vector), with rows corresponding to |
list_snp_id |
List (same length as the number of BGEN files) of
character vector of SNP IDs to read. These should be in the form
|
ind_row |
An optional vector of the row indices (individuals) that
are used. If not specified, all rows are used. |
bgi_dir |
Directory of index files. Default is the same as |
read_as |
How to read BGEN probabilities? Currently implemented:
|
block_size |
Maximum size of temporary blocks (in number of variants).
Default is |
ncores |
Number of cores used. Default doesn't use parallelism.
You may use |
The product bgen_data[ind_row, 'list_snp_id'] %*% beta.
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