liftover_gwas | R Documentation |
Determine GWAS build and liftover to required build
liftover_gwas(
dat,
build = c(37, 38, 36),
to = 37,
chr_col = "chr",
pos_col = "pos",
snp_col = "snp",
ea_col = "ea",
oa_col = "oa",
build_fallback = "position"
)
dat |
Data frame with chr, pos, snp name, effect allele, non-effect allele columns |
build |
The possible builds to check data against Default = c(37,38,26) |
to |
Which build to lift over to. Default=37 |
chr_col |
Name of chromosome column name. Required |
pos_col |
Name of position column name. Required |
snp_col |
Name of SNP column name. Optional. Uses less certain method of matching if not available |
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 |
build_fallback |
Whether to try "position" (fast) or "biomart" (more accurate if you have rsids) based approaches instead |
Data frame
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