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")

Arguments

info_snp

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

liftOver

Path to liftOver executable. Binaries can be downloaded at https://bit.ly/2KvHugi for Mac and at https://bit.ly/2TbSaEI for Linux.

from

Genome build to convert from. Default is hg18.

to

Genome build to convert to. Default is hg19.

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.