get_chain_file: Download chain file for liftover

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

Download chain file for liftover

Description

Download chain file for liftover

Usage

get_chain_file(
  from = c("hg38", "hg19"),
  to = c("hg19", "hg38"),
  chain_source = c("ucsc", "ensembl"),
  save_dir = tempdir(),
  verbose = TRUE
)

Arguments

from	genome build converted from ("hg38", "hg19")
to	genome build converted to ("hg19", "hg38")
chain_source	chain file source used ("ucsc" as default, or "ensembl")
save_dir	where is the chain file saved? Default is a temp directory
verbose	extra messages printed? Default is TRUE

Value

loaded chain file for liftover

Source

UCSC chain files

Ensembl chain files

neurogenomics/MungeSumstats documentation built on Aug. 10, 2024, 5:59 a.m.