@@ -19,3 +19,8 @@ Imports:

     R.utils,

     tools,

     BiocFileCache

+Suggests: 

+    testthat (>= 3.0.0),

+    GenomicRanges,

+    IRanges

+Config/testthat/edition: 3

@@ -2,8 +2,6 @@

 output: github_document

 ---

-<!-- README.md is generated from README.Rmd. Please edit that file -->

-

 ```{r, include = FALSE}

 knitr::opts_chunk$set(

     collapse = TRUE,

@@ -24,16 +22,6 @@ The goal of `easylift` is to perform genomic liftover given `GRanges` and `chain

 ## Installation

-<!-- Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `easylift` from [Bioconductor](http://bioconductor.org/) using the following code: -->

-

-<!-- ```{r 'install', eval = FALSE} -->

-<!-- if (!requireNamespace("BiocManager", quietly = TRUE)) { -->

-<!--     install.packages("BiocManager") -->

-<!-- } -->

-

-<!-- BiocManager::install("easylift") -->

-<!-- ``` -->

-

 Get the latest development version from [GitHub](https://github.com/nahid18/easylift) with:

 ```{r 'install_dev', eval = FALSE}

@@ -41,14 +29,13 @@ BiocManager::install("nahid18/easylift")

 ```

 ## Usage

-First, import the libraries

-```{r library, eval = requireNamespace('easylift', 'GenomicRanges')}

+Import the libraries

+```{r library, eval = FALSE}

 library("easylift")

 library("GenomicRanges")

 ```

-Then, execute the code below. 

-This assumes you already downloaded the required chain file.

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

 ```{r example, eval = FALSE}

 gr <- GRanges(seqname = Rle(paste("chr", 1, sep = "")),

@@ -56,6 +43,7 @@ gr <- GRanges(seqname = Rle(paste("chr", 1, sep = "")),

 genome(gr) <- "hg19"

 to <- "hg38"

 chain <- "hg19ToHg38.over.chain.gz"

+

 lifted <- easylift(gr, to, chain)

 ```

@@ -73,9 +61,9 @@ A BibTeX entry for LaTeX users is

 ```

   @Manual{,

     title = {easylift: An R package to perform genomic liftOver},

-    author = {Abdullah {Al Nahid} and Michael Love},

+    author = {Abdullah Al Nahid and Michael Love},

     year = {2023},

-    note = {R package version 0.0.1},

+    note = {R package version 0.0.2},

     url = {https://github.com/nahid18/easylift},

   }

 ```

@@ -1,6 +1,4 @@

-<!-- README.md is generated from README.Rmd. Please edit that file -->

-

 # easylift

 <!-- badges: start -->

@@ -16,14 +14,6 @@ and `chain` file.

 ## Installation

-<!-- Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `easylift` from [Bioconductor](http://bioconductor.org/) using the following code: -->

-<!-- ```{r 'install', eval = FALSE} -->

-<!-- if (!requireNamespace("BiocManager", quietly = TRUE)) { -->

-<!--     install.packages("BiocManager") -->

-<!-- } -->

-<!-- BiocManager::install("easylift") -->

-<!-- ``` -->

-

 Get the latest development version from

 [GitHub](https://github.com/nahid18/easylift) with:

@@ -33,15 +23,14 @@ BiocManager::install("nahid18/easylift")

 ## Usage

-First, import the libraries

+Import the libraries

 ``` r

 library("easylift")

 library("GenomicRanges")

 ```

-Then, execute the code below. This assumes you already downloaded the

-required chain file.

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

 ``` r

 gr <- GRanges(seqname = Rle(paste("chr", 1, sep = "")),

@@ -49,6 +38,7 @@ gr <- GRanges(seqname = Rle(paste("chr", 1, sep = "")),

 genome(gr) <- "hg19"

 to <- "hg38"

 chain <- "hg19ToHg38.over.chain.gz"

+

 lifted <- easylift(gr, to, chain)

 ```

@@ -64,9 +54,9 @@ A BibTeX entry for LaTeX users is

       @Manual{,

         title = {easylift: An R package to perform genomic liftOver},

-        author = {Abdullah {Al Nahid} and Michael Love},

+        author = {Abdullah Al Nahid and Michael Love},

         year = {2023},

-        note = {R package version 0.0.1},

+        note = {R package version 0.0.2},

         url = {https://github.com/nahid18/easylift},

       }

new file mode 100644

@@ -0,0 +1,12 @@

+# This file is part of the standard setup for testthat.

+# It is recommended that you do not modify it.

+#

+# Where should you do additional test configuration?

+# Learn more about the roles of various files in:

+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview

+# * https://testthat.r-lib.org/articles/special-files.html

+

+library(testthat)

+library(easylift)

+

+test_check("easylift")

new file mode 100644

@@ -0,0 +1,44 @@

+library(GenomicRanges)

+library(IRanges)

+

+test_that("easylift function tests with valid chain files", {

+

+  # Test 1: Test with a valid chain gzipped file

+  chain_path_gz <- system.file("extdata", "hg19ToHg38.over.chain.gz", package = "easylift")

+  gr <- GenomicRanges::GRanges(

+    seqnames = "chr1",

+    ranges = IRanges::IRanges(start = 100, end = 200),

+    strand = "+"

+  )

+  genome(gr) <- "hg19"

+  expect_type(easylift(gr, to = "hg38", chain = chain_path_gz), "S4")

+  expect_no_error(easylift(gr, to = "hg38", chain = chain_path_gz))

+

+  # Test 2: Test with a valid chain file

+  chain_path <- system.file("extdata", "hg19ToHg38.over.chain", package = "easylift")

+  gr2 <- GenomicRanges::GRanges(

+    seqnames = "chr2",

+    ranges = IRanges::IRanges(start = 200, end = 300),

+    strand = "+"

+  )

+  genome(gr2) <- "hg19"

+  expect_type(easylift(gr2, to = "hg38", chain = chain_path), "S4")

+  expect_no_error(easylift(gr2, to = "hg38", chain = chain_path))

+

+})

+

+test_that("easylift function tests with error cases", {

+

+  # Test 3: Test with an empty GRanges object

+  gr3 <- GenomicRanges::GRanges()

+  expect_error(easylift(gr3, to = "hg38", chain = chain_path))

+

+  # Test 4: Test with missing genome information

+  gr4 <- GenomicRanges::GRanges(

+    seqnames = "chr4",

+    ranges = IRanges::IRanges(start = 400, end = 500),

+    strand = "+"

+  )

+  expect_error(easylift(gr4, to = "hg38", chain = chain_path))

+

+})