# easylift
 
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 The goal of `easylift` is to perform genomic liftover given `GRanges`
 and `chain` file.
 

 ## Installation

 
 ``` r

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

 BiocManager::install("easylift")

 ```
 

 ## Documentation
 
 To view documentation:
 
 ``` r
 browseVignettes("easylift")
 ```
 
 ## Import

 Import the libraries

 
 ``` r
 library("easylift")
 ```
 

 Call `easylift` with `GRanges` object, target genome and the chain file.

 
 ``` r

 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

 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

 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.