Transfer genomic coordinates from one genome build to another.
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", verbose = TRUE )
data table obj of the summary statistics file for the GWAS.
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).
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 file source used ("ucsc" as default, or "ensembl")
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.
Name of the chromosome column in
sumstats_dt (e.g. "CHR").
Name of the starting genomic position
sumstats_dt (e.g. "POS","start").
Name of the ending genomic position
sumstats_dt (e.g. "POS","end").
Can be the same as
only contains SNPs that span 1 base pair (bp) each.
Style to return GRanges object in
(e.g. "NCBI" = 4; "UCSC" = "chr4";) (default:
Lifted summary stats in
or GRanges format.
sumstats_dt <- MungeSumstats::formatted_example() #> Standardising column headers. #> First line of summary statistics file: #> MarkerName CHR POS A1 A2 EAF Beta SE Pval #> Sorting coordinates. sumstats_dt_hg38 <- liftover(sumstats_dt=sumstats_dt, ref_genome = "hg19", convert_ref_genome="hg38") #> Performing data liftover from hg19 to hg38. #> Converting summary statistics to Genomic Ranges. #> Downloading chain file from Ensembl. #> /tmp/RtmpmswcRa/GRCh37_to_GRCh38.chain.gz #> Reordering so first three column headers are SNP, CHR and BP in this order. #> Reordering so the fourth and fifth columns are A1 and A2.