From bc934721490c6d8b75b4e98aaf72b7a8828827ac Mon Sep 17 00:00:00 2001
From: mattssca <mattsada@gmail.com>
Date: Mon, 5 Feb 2024 13:03:49 -0800
Subject: [PATCH 1/8] New unit tests and minor improvements

---
 R/bin_splitter.R                    |  4 ++--
 man/bin_splitter.Rd                 |  2 +-
 tests/testthat/test-bin_splitter.R  | 29 +++++++++++++++++++++++++++++
 tests/testthat/test-get_gene_info.R |  2 +-
 4 files changed, 33 insertions(+), 4 deletions(-)
 create mode 100644 tests/testthat/test-bin_splitter.R

diff --git a/R/bin_splitter.R b/R/bin_splitter.R
index 70b18f3..8acd7d0 100644
--- a/R/bin_splitter.R
+++ b/R/bin_splitter.R
@@ -4,7 +4,7 @@
 #' specified size.
 #' 
 #' @details This function internally calls the purify_regions function to 
-#' properly format the incoming regions.Thus, thuis function can accept either a 
+#' properly format the incoming regions.Thus, this function can accept either a 
 #' data frame of regions or individual region coordinates.
 #'
 #' @param these_regions The region(s) to be queried. Can be a data frame with
@@ -39,7 +39,7 @@ bin_splitter = function(these_regions = NULL,
                         qend = NULL,
                         bin_size = 1000){
   
-  #call helperto format regions
+  #call helper to format regions
   my_regions = purify_regions(these_regions = these_regions,
                               qchrom = qchrom,
                               qstart = qstart,
diff --git a/man/bin_splitter.Rd b/man/bin_splitter.Rd
index 5cde8f4..a4c9134 100644
--- a/man/bin_splitter.Rd
+++ b/man/bin_splitter.Rd
@@ -35,7 +35,7 @@ specified size.
 }
 \details{
 This function internally calls the purify_regions function to 
-properly format the incoming regions.Thus, thuis function can accept either a 
+properly format the incoming regions.Thus, this function can accept either a 
 data frame of regions or individual region coordinates.
 }
 \examples{
diff --git a/tests/testthat/test-bin_splitter.R b/tests/testthat/test-bin_splitter.R
new file mode 100644
index 0000000..f584065
--- /dev/null
+++ b/tests/testthat/test-bin_splitter.R
@@ -0,0 +1,29 @@
+#load packages
+library(testthat)
+
+test_that("bin_splitter returns correct number of bins", {
+  result <- bin_splitter(qchrom = c("chr1"), qstart = c(1), qend = c(1001), bin_size = 100)
+  expect_equal(nrow(result), 10)
+})
+
+test_that("bin_splitter returns correct bin size", {
+  result <- bin_splitter(qchrom = c("chr1"), qstart = c(1), qend = c(1000), bin_size = 100)
+  expect_equal(result$bin_end[1] - result$bin_start[1], 100)
+})
+
+test_that("bin_splitter handles multiple regions", {
+  result <- bin_splitter(qchrom = c("chr1", "chr2"), qstart = c(1, 1001), qend = c(1001, 2001), bin_size = 100)
+  expect_equal(nrow(result), 20)
+})
+
+test_that("bin_splitter handles regions data frame", {
+  my_regions <- data.frame(chrom = c("chr1", "chr2"), start = c(1, 1000), end = c(1001, 2001))
+  result <- bin_splitter(these_regions = my_regions, bin_size = 100)
+  expect_equal(nrow(result), 20)
+})
+
+test_that("bin_splitter returns correct chromosome names", {
+  result <- bin_splitter(qchrom = c("chr1", "chr2"), qstart = c(1, 1001), qend = c(1000, 2000), bin_size = 100)
+  expect_equal(unique(result$bin_chr), c("chr1", "chr2"))
+})
+
diff --git a/tests/testthat/test-get_gene_info.R b/tests/testthat/test-get_gene_info.R
index 5736524..4abcfec 100644
--- a/tests/testthat/test-get_gene_info.R
+++ b/tests/testthat/test-get_gene_info.R
@@ -1,4 +1,4 @@
-#load pacakges
+#load packages
 library(testthat)
 
 

From 24612ea322b615cdcc18542017c504471fdea645 Mon Sep 17 00:00:00 2001
From: mattssca <mattsada@gmail.com>
Date: Mon, 5 Feb 2024 13:05:51 -0800
Subject: [PATCH 2/8] Updated gitignore

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 671b0d8..3a14286 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,3 @@
 .Rproj.user
 .DS_Store
+my_bed.bed
\ No newline at end of file

From 4cf255b49f698de8fc2fbd125d0abb89599e5567 Mon Sep 17 00:00:00 2001
From: mattssca <mattsada@gmail.com>
Date: Mon, 5 Feb 2024 13:21:11 -0800
Subject: [PATCH 3/8] Adding outstanding unit tests

---
 tests/testthat/test-gene_ranger.R          | 23 +++++++++++
 tests/testthat/test-purify_chr.R           | 25 ++++++++++++
 tests/testthat/test-purify_regions.R       | 47 ++++++++++++++++++++++
 tests/testthat/test-region_ranger.R        | 23 +++++++++++
 tests/testthat/test-sanity_check_regions.R | 31 ++++++++++++++
 5 files changed, 149 insertions(+)
 create mode 100644 tests/testthat/test-gene_ranger.R
 create mode 100644 tests/testthat/test-purify_chr.R
 create mode 100644 tests/testthat/test-region_ranger.R
 create mode 100644 tests/testthat/test-sanity_check_regions.R

diff --git a/tests/testthat/test-gene_ranger.R b/tests/testthat/test-gene_ranger.R
new file mode 100644
index 0000000..e617796
--- /dev/null
+++ b/tests/testthat/test-gene_ranger.R
@@ -0,0 +1,23 @@
+library(testthat)
+
+test_that("gene_ranger throws error with no genes", {
+  expect_error(gene_ranger())
+})
+
+test_that("gene_ranger throws error with invalid projection", {
+  expect_error(gene_ranger(these_genes = "MYC", projection = "invalid"))
+})
+
+test_that("gene_ranger throws error with invalid return format", {
+  expect_error(gene_ranger(these_genes = "MYC", return_as = "invalid"))
+})
+
+test_that("gene_ranger throws error when write_to_bed is TRUE but bed_path, track_name, or track_description is not provided", {
+  expect_error(gene_ranger(these_genes = "MYC", write_to_bed = TRUE), "Provide a path for output bed file")
+  expect_error(gene_ranger(these_genes = "MYC", write_to_bed = TRUE, bed_path = "my_bed"), "Provide a track name for output bed file")
+  expect_error(gene_ranger(these_genes = "MYC", write_to_bed = TRUE, bed_path = "my_bed", track_name = "MYC"), "Provide a track description for output bed file")
+})
+
+test_that("gene_ranger runs successfully with valid input", {
+  expect_silent(gene_ranger(these_genes = "MYC"))
+})
diff --git a/tests/testthat/test-purify_chr.R b/tests/testthat/test-purify_chr.R
new file mode 100644
index 0000000..31fcb3d
--- /dev/null
+++ b/tests/testthat/test-purify_chr.R
@@ -0,0 +1,25 @@
+library(testthat)
+
+test_that("purify_chr throws error with no projection", {
+  expect_error(purify_chr(), "You must provide a valid projection")
+})
+
+test_that("purify_chr throws error with no incoming_table", {
+  expect_error(purify_chr(projection = "hg38"), "You must provide a data table with `incoming_table`")
+})
+
+test_that("purify_chr throws error with invalid projection", {
+  expect_error(purify_chr(projection = "invalid", incoming_table = data.frame(chrom = c("1", "2", "3"))), "This function supports the following projections")
+})
+
+test_that("purify_chr adds 'chr' prefix for hg38 projection", {
+  df = data.frame(chrom = c("1", "2", "3"))
+  result = purify_chr(projection = "hg38", incoming_table = df)
+  expect_equal(result$chrom, c("chr1", "chr2", "chr3"))
+})
+
+test_that("purify_chr removes 'chr' prefix for grch37 projection", {
+  df = data.frame(chrom = c("chr1", "chr2", "chr3"))
+  result = purify_chr(projection = "grch37", incoming_table = df)
+  expect_equal(result$chrom, c("1", "2", "3"))
+})
diff --git a/tests/testthat/test-purify_regions.R b/tests/testthat/test-purify_regions.R
index e69de29..ccd66e3 100644
--- a/tests/testthat/test-purify_regions.R
+++ b/tests/testthat/test-purify_regions.R
@@ -0,0 +1,47 @@
+library(testthat)
+
+test_that("purify_regions handles single region string", {
+  result <- purify_regions(these_regions = "chr1:100-500")
+  expect_equal(nrow(result), 1)
+  expect_equal(result$chrom, "chr1")
+  expect_equal(result$start, 100)
+  expect_equal(result$end, 500)
+})
+
+test_that("purify_regions handles multiple region strings", {
+  result <- purify_regions(these_regions = c("chr1:100-500", "chr2:100-500"))
+  expect_equal(nrow(result), 2)
+  expect_equal(result$chrom, c("chr1", "chr2"))
+  expect_equal(result$start, c(100, 100))
+  expect_equal(result$end, c(500, 500))
+})
+
+test_that("purify_regions handles individual region parameters", {
+  result <- purify_regions(qchrom = "chr1", qstart = 100, qend = 500)
+  expect_equal(nrow(result), 1)
+  expect_equal(result$chrom, "chr1")
+  expect_equal(result$start, 100)
+  expect_equal(result$end, 500)
+})
+
+test_that("purify_regions handles multiple individual region parameters", {
+  result <- purify_regions(qchrom = c("chr1", "chr2"), qstart = c(100, 200), qend = c(500, 600))
+  expect_equal(nrow(result), 2)
+  expect_equal(result$chrom, c("chr1", "chr2"))
+  expect_equal(result$start, c(100, 200))
+  expect_equal(result$end, c(500, 600))
+})
+
+test_that("purify_regions handles data frame input", {
+  my_regions <- data.frame(chrom = c("chr1", "chr2"), start = c(100, 200), end = c(500, 600))
+  result <- purify_regions(these_regions = my_regions)
+  expect_equal(nrow(result), 2)
+  expect_equal(result$chrom, c("chr1", "chr2"))
+  expect_equal(result$start, c(100, 200))
+  expect_equal(result$end, c(500, 600))
+})
+
+test_that("purify_regions throws error with incorrect input", {
+  expect_error(purify_regions(qchrom = "chr1", qstart = 100))
+  expect_error(purify_regions(these_regions = data.frame(chrom = c("chr1", "chr2"), start = c(100, 200), end = c(50, 100))))
+})
diff --git a/tests/testthat/test-region_ranger.R b/tests/testthat/test-region_ranger.R
new file mode 100644
index 0000000..8dce8ee
--- /dev/null
+++ b/tests/testthat/test-region_ranger.R
@@ -0,0 +1,23 @@
+library(testthat)
+
+test_that("region_ranger throws error with no regions", {
+  expect_error(region_ranger())
+})
+
+test_that("region_ranger throws error with invalid projection", {
+  expect_error(region_ranger(these_regions = "chr8:127735434-127742951", projection = "invalid"), "This function supports the following projections")
+})
+
+test_that("region_ranger returns correct number of columns when raw is FALSE", {
+  result = region_ranger(these_regions = "chr8:127735434-127742951")
+  expect_equal(ncol(result), 11)
+})
+
+test_that("region_ranger returns all columns when raw is TRUE", {
+  result = region_ranger(these_regions = "chr8:127735434-127742951", raw = TRUE)
+  expect_true(ncol(result) > 11)
+})
+
+test_that("region_ranger returns warning when no genes found", {
+  expect_warning(region_ranger(these_regions = "chr1:1-10"))
+})
diff --git a/tests/testthat/test-sanity_check_regions.R b/tests/testthat/test-sanity_check_regions.R
new file mode 100644
index 0000000..9d55699
--- /dev/null
+++ b/tests/testthat/test-sanity_check_regions.R
@@ -0,0 +1,31 @@
+library(testthat)
+
+test_that("sanity_check_regions throws error with no regions", {
+  expect_error(sanity_check_regions(), "No regions provided")
+})
+
+test_that("sanity_check_regions throws error with invalid projection", {
+  my_regions <- data.frame(chrom = c("chr1"), start = c(100), end = c(200))
+  expect_error(sanity_check_regions(incoming_regions = my_regions, projection = "invalid"), "Invalid projection specified")
+})
+
+test_that("sanity_check_regions throws error when start is greater than end", {
+  my_regions <- data.frame(chrom = c("chr1"), start = c(200), end = c(100))
+  expect_error(sanity_check_regions(incoming_regions = my_regions, projection = "hg38"), "start is greater than or equal to end")
+})
+
+test_that("sanity_check_regions throws error when start or end is outside chromosomal range", {
+  my_regions <- data.frame(chrom = c("chr1"), start = c(100), end = c(300000000))
+  expect_error(sanity_check_regions(incoming_regions = my_regions, projection = "hg38"), "Specified start or end coordinates fall outside the actual chromosomal range")
+})
+
+test_that("sanity_check_regions runs successfully with valid input", {
+  my_regions <- data.frame(chrom = c("chr1"), start = c(100), end = c(200))
+  expect_silent(sanity_check_regions(incoming_regions = my_regions, projection = "hg38"))
+})
+
+test_that("sanity_check_regions runs successfully with valid input", {
+  my_regions <- data.frame(chrom = c("1"), start = c(100), end = c(200))
+  expect_silent(sanity_check_regions(incoming_regions = my_regions, projection = "grch37"))
+})
+

From 30ef315dec8cf566c666c15d2dd65ce002bcbfd0 Mon Sep 17 00:00:00 2001
From: mattssca <mattsada@gmail.com>
Date: Mon, 5 Feb 2024 13:32:34 -0800
Subject: [PATCH 4/8] Updated README

---
 README.md | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index 4286b52..80e9d5e 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,5 @@
 # BioMaesteR
-A package with convenience functions for generic genomic analysis within R. 
-Standardized, generic functions as well as bundled data objects that can be 
-called in various settings in the scope of biological analysis in R. 
-This package is specialized to provide bioinformatics infrastructure that can be 
-used in a variety of analysis. 
\ No newline at end of file
+This is BioMaesteR, an R package with convenience functions commonly requested in various types of genomic analysis within R. This package is specialized to provide bioinformatics infrastructure that can be 
+used in a variety of genomic analysis. 
+
+This repo is also an ongoing project intended for demonstrating and following best-practices in development of R packages. This includes adequate package documentation (functions, bundled data objects, etc.), reproducible unit tests and vignettes. Upon Pull Requests, this repo also executes a GitAction workflow where the package is installed in various environments and thorough testing of the complete code base.
\ No newline at end of file

From 582829764c768b7e831fb505fe28b335e089080e Mon Sep 17 00:00:00 2001
From: mattssca <mattsada@gmail.com>
Date: Mon, 5 Feb 2024 14:04:09 -0800
Subject: [PATCH 5/8] adding logo

---
 biomaesteR.png | Bin 0 -> 15709 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 biomaesteR.png

diff --git a/biomaesteR.png b/biomaesteR.png
new file mode 100644
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HcmV?d00001


From ba8fc2669c9dd0986385470ac9e7e28217cc9809 Mon Sep 17 00:00:00 2001
From: mattssca <mattsada@gmail.com>
Date: Mon, 5 Feb 2024 14:05:02 -0800
Subject: [PATCH 6/8] new line at the end of gitignore

---
 .gitignore | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 3a14286..23a20d4 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,3 @@
 .Rproj.user
 .DS_Store
-my_bed.bed
\ No newline at end of file
+my_bed.bed

From 7216fe5265c4c50a211c779c314ed8d269b95105 Mon Sep 17 00:00:00 2001
From: mattssca <mattsada@gmail.com>
Date: Mon, 5 Feb 2024 14:06:29 -0800
Subject: [PATCH 7/8] adding logo

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index 80e9d5e..509dcfb 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,4 @@
+# <img src="biomaesteR.png" align="right" alt="" width="120" />
 # BioMaesteR
 This is BioMaesteR, an R package with convenience functions commonly requested in various types of genomic analysis within R. This package is specialized to provide bioinformatics infrastructure that can be 
 used in a variety of genomic analysis. 

From 008bb0a7c605d9906574b230ce72a4f9b2d7a199 Mon Sep 17 00:00:00 2001
From: mattssca <mattsada@gmail.com>
Date: Mon, 5 Feb 2024 14:07:24 -0800
Subject: [PATCH 8/8] Readme updates

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 509dcfb..a79e8b1 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
 # <img src="biomaesteR.png" align="right" alt="" width="120" />
-# BioMaesteR
-This is BioMaesteR, an R package with convenience functions commonly requested in various types of genomic analysis within R. This package is specialized to provide bioinformatics infrastructure that can be 
+# biomaesteR
+This is biomaesteR, an R package with convenience functions commonly requested in various types of genomic analysis within R. This package is specialized to provide bioinformatics infrastructure that can be 
 used in a variety of genomic analysis. 
 
 This repo is also an ongoing project intended for demonstrating and following best-practices in development of R packages. This includes adequate package documentation (functions, bundled data objects, etc.), reproducible unit tests and vignettes. Upon Pull Requests, this repo also executes a GitAction workflow where the package is installed in various environments and thorough testing of the complete code base.
\ No newline at end of file