Genome build liftover

Transfer genomic coordinates from one genome build to another.

liftover(
  sumstats_dt,
  convert_ref_genome = NULL,
  ref_genome = NULL,
  chrom_col = "CHR",
  start_col = "POS",
  end_col = start_col,
  as_granges = FALSE,
  style = "NCBI",
  verbose = TRUE
)

Source

liftOver

UCSC chain files

Arguments

sumstats_dt

data table of the GWAS/QTL summary statistics.

convert_ref_genome

name of the reference genome to convert to ("GRCh37" or "GRCh38"). This will only occur if the current genome build does not match. Default is not to convert the genome build (NULL).

ref_genome

name of the reference genome used for the GWAS ("GRCh37" or "GRCh38"). Argument is case-insensitive. Default is NULL which infers the reference genome from the data.

chrom_col

column for chromosome

start_col

column for start position

end_col

column for end position (is the same as start for snps)

as_granges

Return results as GRanges.

style

GRanges style (e.g. "UCSC" = "chr4; "NCBI" = 4).

verbose

Print messages.

Value

Lifted summary stats data.table