Imputation

Source: R/external-software.R

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
)

Arguments

beagle.path

Path to the executable of Beagle v4+.

plink.path

Path to the executable of PLINK 1.9.

bedfile.in

Path to the input bedfile.

bedfile.out

Path to the output bedfile. Default is created by appending "_impute" to prefix.in (bedfile.in without extension).

memory.max

Max memory (in GB) to be used. It is internally rounded to be an integer. Default is 3.

ncores

Number of cores used. Default doesn't use parallelism. You may use bigstatsr::nb_cores().

extra.options

Other options to be passed to Beagle as a string. More options can be found at Beagle's website.

plink.options

Other options to be passed to PLINK as a string. More options can be found at https://www.cog-genomics.org/plink2/filter.

verbose

Whether to show PLINK log? Default is TRUE.

Value

The path of the new bedfile.

Details

Downloads and more information can be found at the following websites

References

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.