Liftover GWAS positions
lift.RdDetermine GWAS build and liftover to required build. This is the same function from the GwasDataImport package, the only difference being that you can specify the build rather than it trying to guess the build (which fails if you are trying to liftover small segments of the genome).
Usage
lift(
gwas,
from = "Hg19",
to = "Hg38",
snp_col = "snp",
chr_col = "chr",
pos_col = "pos",
ea_col = "ea",
oa_col = "oa",
remove_duplicates = TRUE
)Arguments
- gwas
a data.table, or file path, chr, pos, snp name, effect allele, non-effect allele columns
- from
which build to lift from, one of c("Hg18", "Hg19", "Hg38")
- to
which build to lift over to, one of c("Hg18", "Hg19", "Hg38")
- snp_col
Name of SNP column name. Optional. Uses less certain method of matching if not available
- chr_col
Name of chromosome column name. Required
- pos_col
Name of position column name. Required
- ea_col
Name of effect allele column name. Optional. Might lead to duplicated rows if not presented
- oa_col
Name of other allele column name. Optional. Might lead to duplicated rows if not presented
- remove_duplicates
a logical, whether to remove duplicate IDs