easylift

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.

Installation

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

BiocManager::install("easylift")

Documentation

To view documentation:

browseVignettes("easylift")

Import

Import the libraries

library("easylift")

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
  )
)
# "hg19" is the source genome
genome(gr) <- "hg19"
# chain file path
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.