GitHub - nahid18/easylift: Perform genomic liftover (original) (raw)

easylift

The goal of easylift is to perform genomic liftover given GRangesand chain file. easylift was developed as part of thetidyomics project'sopen challenges.

Installation

if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("easylift")

Documentation

To view documentation:

browseVignettes("easylift")

Import

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)

BiocFileCache

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")

Citation

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.

Code of Conduct

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.