snp_modifyBuild {bigsnpr}

Modify genome build

Description

Modify the physical position information of a data frame when converting genome build using executable liftOver.

Usage

snp_modifyBuild(
  info_snp,
  liftOver,
  from = "hg18",
  to = "hg19",
  check_reverse = TRUE
)

Arguments

info_snp

A data frame with columns "chr" and "pos".

liftOver

Path to liftOver executable. Binaries can be downloaded at https://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/liftOver for Mac and at https://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver for Linux.

from

Genome build to convert from. Default is hg18.

to

Genome build to convert to. Default is hg19.

check_reverse

Whether to discard positions for which we cannot go back to initial values by doing 'from -> to -> from'. Default is TRUE.

Value

Input data frame info_snp with column "pos" in the new build.

References

Hinrichs, Angela S., et al. "The UCSC genome browser database: update 2006." Nucleic acids research 34.suppl_1 (2006): D590-D598.