README.Rmd

---
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.