Imputation using Beagle version 4.
snp_beagleImpute(
beagle.path,
plink.path,
bedfile.in,
bedfile.out = NULL,
memory.max = 3,
ncores = 1,
extra.options = "",
plink.options = "",
verbose = TRUE
)The path of the new bedfile.
Path to the executable of Beagle v4+.
Path to the executable of PLINK 1.9.
Path to the input bedfile.
Path to the output bedfile. Default is created by
appending "_impute" to prefix.in (bedfile.in without extension).
Max memory (in GB) to be used. It is internally rounded
to be an integer. Default is 3.
Number of cores used. Default doesn't use parallelism. You may use nb_cores.
Other options to be passed to Beagle as a string. More options can be found at Beagle's website.
Other options to be passed to PLINK as a string. More options can be found at https://www.cog-genomics.org/plink2/filter.
Whether to show PLINK log? Default is TRUE.
Downloads and more information can be found at the following websites
Browning, Brian L., and Sharon R. Browning. "Genotype imputation with millions of reference samples." The American Journal of Human Genetics 98.1 (2016): 116-126.
download_plink download_beagle