Genome build liftover

Transfer genomic coordinates from one genome build to another.

Usage

liftover(
  dat,
  query_genome,
  target_genome,
  query_chrom_col = "CHR",
  query_start_col = "POS",
  query_end_col = query_start_col,
  pos_prefix = "POS",
  as_granges = FALSE,
  style = "NCBI",
  verbose = TRUE
)

Source

liftOver

UCSC chain files

Arguments

dat

data.table of GWAS/QTL summary statistics.

query_genome

name of the reference genome used for the GWAS (e.g. "GRCh37" or "GRCh38"). Argument is case-insensitive.

target_genome

name of the reference genome to convert to ("GRCh37" or "GRCh38"). This will only occur if the query_genome does not match the target_genome.

query_chrom_col

Name of the chromosome column in query_dat (e.g. "CHR").

query_start_col

Name of the starting genomic position column in query_dat (e.g. "POS","start").

query_end_col

Name of the ending genomic position column in query_dat (e.g. "POS","end"). Can be the same as query_start_col when query_dat only contains SNPs that span 1 base pair (bp) each.

pos_prefix

After the start_colend_col has been lifted over, how should these columns be named?

as_granges

Return results as GRanges instead of a data.table (default: FALSE).

style

Style to return GRanges object in (e.g. "NCBI" = 4; "UCSC" = "chr4";) (default: "NCBI").

verbose

Print messages.

Value

Lifted summary stats in data.table or GRanges format.

See also

Other liftover functions: get_chain_file()

Examples

if (FALSE) { # \dontrun{
dat <- echodata::BST1
#### hg19 ==> hg38 ####
dat_lifted <- liftover(
    dat = dat,
    query_genome = "hg19",
    target_genome = "hg38"
)
} # }