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Remap genomic coordinates to a different genome assembly

Source: R/liftover.R
liftover.Rd

Converts SummarySet GWAS summary data to a different genome assembly. Human genome chain files are download from ENSEMBL

Usage

liftover(summaryset, chainfile = NULL, to = "GRCh38")

Arguments

summaryset

A gwasglue2 SummarySet object

chainfile

The chainfile used to remap the genomic coordinates. If NULL a chainfile is downloaded using the to and the summarysetmetadata to check the genome assembly to which GWAS summary data is currently mapped.

to

genome assembly to which should be mapped. Default "GRCh38"

  • Other options: "NCBI34", "NCBI35", "NCBI36", GRCh37" and "GRCh38"

Value

A gwasglue2 SummarySet object with GWAS summary data genomic coordinates remapped.

See also

create_metadata() and addToMetadata() on how to create or add to metadata. Note that if using chainfile the analyses are not restricted to Human GWAS.