liftover: Genome build liftover

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

Genome build liftover

Description

Transfer genomic coordinates from one genome build to another.

Usage

liftover(
  sumstats_dt,
  convert_ref_genome,
  ref_genome,
  chain_source = "ensembl",
  imputation_ind = TRUE,
  chrom_col = "CHR",
  start_col = "BP",
  end_col = start_col,
  as_granges = FALSE,
  style = "NCBI",
  local_chain = NULL,
  verbose = TRUE
)

Arguments

sumstats_dt	data table obj of the summary statistics file for the GWAS.
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.
chain_source	chain file source used ("ucsc" as default, or "ensembl")
imputation_ind	Binary Should a column be added for each imputation step to show what SNPs have imputed values for differing fields. This includes a field denoting SNP allele flipping (flipped). On the flipped value, this denoted whether the alelles where switched based on MungeSumstats initial choice of A1, A2 from the input column headers and thus may not align with what the creator intended.Note these columns will be in the formatted summary statistics returned. Default is FALSE.
chrom_col	Name of the chromosome column in sumstats_dt (e.g. "CHR").
start_col	Name of the starting genomic position column in sumstats_dt (e.g. "POS","start").
end_col	Name of the ending genomic position column in sumstats_dt (e.g. "POS","end"). Can be the same as start_col when sumstats_dt only contains SNPs that span 1 base pair (bp) each.
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").
local_chain	Path to local chain file to use instead of downlaoding. Default of NULL i.e. no local file to use. NOTE if passing a local chain file make sure to specify the path to convert from and to the correct build like GRCh37 to GRCh38. We can not sense check this for local files. The chain file can be submitted as a gz file (as downloaed from source) or unzipped.
verbose	Print messages.

Value

Lifted summary stats in data.table or GRanges format.

Source

liftOver

UCSC chain files

Ensembl chain files

Examples

sumstats_dt <- MungeSumstats::formatted_example()

sumstats_dt_hg38 <- liftover(sumstats_dt=sumstats_dt, 
                             ref_genome = "hg19",
                             convert_ref_genome="hg38")

neurogenomics/MungeSumstats documentation built on May 2, 2024, 9:04 a.m.