snp_beagleImpute: Imputation

In bigsnpr: Analysis of Massive SNP Arrays

Imputation

Description

Imputation using Beagle version 4.

Usage

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.

Details

Downloads and more information can be found at the following websites

• PLINK,

• Beagle.

Value

The path of the new bedfile.

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.

See Also

download_plink download_beagle

bigsnpr documentation built on Sept. 30, 2024, 9:18 a.m.