View source: R/modify-positions.R
snp_modifyBuild | R Documentation |
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/"
)
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 |
to |
Genome build to convert to. Default is |
check_reverse |
Whether to discard positions for which we cannot go back
to initial values by doing 'from -> to -> from'. Default is |
local_chain |
Local chain file (e.g. |
base_url |
From where to download the chain files. Default is
|
Input data frame info_snp
with column "pos" in the new build.
Hinrichs, Angela S., et al. "The UCSC genome browser database: update 2006." Nucleic acids research 34.suppl_1 (2006): D590-D598.
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