An R/Bioconductor library to perform genomic liftover between different genome assemblies with GRanges and chain file. Source Code: https://github.com/nahid18/easylift
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("easylift")To view documentation:
browseVignettes("easylift")library("easylift")
#> Loading required package: GenomicRanges
#> Loading required package: stats4
#> Loading required package: BiocGenerics
#>
#> Attaching package: 'BiocGenerics'
#> The following objects are masked from 'package:stats':
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#> duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
#> lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
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#> The following object is masked from 'package:utils':
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#> Loading required package: IRanges
#> Loading required package: GenomeInfoDb
#> Loading required package: BiocFileCache
#> Loading required package: dbplyrCreate a GRanges object, assign a genome to it, and specify 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"
# Here, we use the `system.file()` function because the chain file is in the
# package (however if you need to point to any other file on your machine,
# just do 'chain <- "path/to/your/hg19ToHg38.over.chain.gz"'):
chain <- system.file("extdata", "hg19ToHg38.over.chain.gz", package = "easylift")
gr
#> GRanges object with 200000 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] chr1 1-200000 *
#> [2] chr1 1-200000 *
#> [3] chr1 1-200000 *
#> [4] chr1 1-200000 *
#> [5] chr1 1-200000 *
#> ... ... ... ...
#> [199996] chr2 1-200000 *
#> [199997] chr2 1-200000 *
#> [199998] chr2 1-200000 *
#> [199999] chr2 1-200000 *
#> [200000] chr2 1-200000 *
#> -------
#> seqinfo: 2 sequences from hg19 genome; no seqlengthsCall easylift with GRanges object, target genome and the chain file.
# Here, "hg38" is the target genome
easylift(gr, "hg38", chain)
#> GRanges object with 300000 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] chr1 10001-177376 *
#> [2] chr19 242824-242864 *
#> [3] chr1 10001-177376 *
#> [4] chr19 242824-242864 *
#> [5] chr1 10001-177376 *
#> ... ... ... ...
#> [299996] chr2 10001-200000 *
#> [299997] chr2 10001-200000 *
#> [299998] chr2 10001-200000 *
#> [299999] chr2 10001-200000 *
#> [300000] chr2 10001-200000 *
#> -------
#> seqinfo: 25 sequences (1 circular) from hg38 genomeTo 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.
sessionInfo()
#> R version 4.3.1 (2023-06-16)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 22.04.3 LTS
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#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
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#> time zone: America/New_York
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#> attached base packages:
#> [1] stats4 stats graphics grDevices utils datasets methods
#> [8] base
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#> other attached packages:
#> [1] easylift_1.0.0 BiocFileCache_2.10.0 dbplyr_2.3.4
#> [4] GenomicRanges_1.54.0 GenomeInfoDb_1.38.0 IRanges_2.36.0
#> [7] S4Vectors_0.40.0 BiocGenerics_0.48.0 BiocStyle_2.30.0
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#> [1] SummarizedExperiment_1.32.0 rjson_0.2.21
#> [3] xfun_0.40 bslib_0.5.1
#> [5] lattice_0.22-5 Biobase_2.62.0
#> [7] vctrs_0.6.4 tools_4.3.1
#> [9] bitops_1.0-7 generics_0.1.3
#> [11] parallel_4.3.1 curl_5.1.0
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#> [17] pkgconfig_2.0.3 R.oo_1.25.0
#> [19] Matrix_1.6-1.1 lifecycle_1.0.3
#> [21] GenomeInfoDbData_1.2.11 compiler_4.3.1
#> [23] Rsamtools_2.18.0 Biostrings_2.70.0
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#> [57] bit_4.0.5 R.methodsS3_1.8.2
#> [59] memoise_2.0.1 evaluate_0.22
#> [61] knitr_1.44 BiocIO_1.12.0
#> [63] rtracklayer_1.62.0 rlang_1.1.1
#> [65] glue_1.6.2 DBI_1.1.3
#> [67] BiocManager_1.30.22 jsonlite_1.8.7
#> [69] R6_2.5.1 MatrixGenerics_1.14.0
#> [71] GenomicAlignments_1.38.0 zlibbioc_1.48.0