The goal of easylift is to perform genomic liftover given GRanges and chain file. easylift was developed as part of the tidyomics project's open challenges.
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("easylift")
To view documentation:
browseVignettes("easylift")
Import the libraries
Call easylift with GRanges object, target genome and the chain file.
gr <- GRanges(
seqname = Rle(
c("chr1", "chr2"),
c(100000, 100000)
),
ranges = IRanges(
start = 1,
end = 200000
)
)
# Here, "hg19" is the source genome
genome(gr) <- "hg19"
chain <- "hg19ToHg38.over.chain.gz"
# Here, "hg38" is the target genome
easylift(gr, "hg38", chain)
To use BiocFileCache for the chain file, add it to the cache:
chain_file <- "/path/to/your/hg19ToHg38.over.chain.gz"
bfc <- BiocFileCache()
# Add chain file to cache if already not available
if (nrow(bfcquery(bfc, basename(chain_file))) == 0)
bfcadd(bfc, chain_file)
Then, use it in easylift:
easylift(gr, "hg38")
# or
gr |> easylift("hg38")
To cite package easylift in publications use:
Al Nahid A, Pagès H, Love M (2023). easylift: An R package to perform genomic liftover. R package version 1.0.0, https://github.com/nahid18/easylift.
A BibTeX entry for LaTeX users is
@Manual{,
title = {easylift: An R package to perform genomic liftover},
author = {Abdullah Al Nahid, Hervé Pagès, Michael Love},
year = {2023},
note = {R package version 1.0.0},
url = {https://github.com/nahid18/easylift},
}
Please note that the easylift was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.
Please note that the easylift project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
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