---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# easylift
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The goal of `easylift` is to perform genomic liftover given `GRanges` and `chain` file.
## Installation
```{r 'install_dev', eval = FALSE}
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("easylift")
```
## Documentation
To view documentation:
```{r doc, eval = FALSE}
browseVignettes("easylift")
```
## Import
Import the libraries
```{r library, eval = FALSE}
library("easylift")
```
Call `easylift` with `GRanges` object, target genome and the chain file.
```{r example, eval = FALSE}
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:
```{r example2, eval = FALSE}
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`:
```{r example3, eval = FALSE}
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](http://bioconductor.org/about/code-of-conduct/). By contributing to this project, you agree to abide by its terms.
