Modify genome build — snp_modifyBuild • bigsnpr

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

snp_modifyBuild(
  info_snp,
  liftOver,
  from = "hg18",
  to = "hg19",
  check_reverse = TRUE,
  local_chain = NULL,
  base_url = "https://hgdownload.soe.ucsc.edu/goldenPath/"
)

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.
local_chain: Local chain file (e.g. hg18ToHg19.over.chain.gz) to use instead of downloading one from parameters from and to (the default). You can download one such file from e.g. https://hgdownload.soe.ucsc.edu/goldenPath/hg18/liftOver/. Provide a vector of two when using check_reverse.
base_url: From where to download the chain files. Default is "https://hgdownload.soe.ucsc.edu/goldenPath/". You can also try replacing https by http, and/or soe by cse.

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.