Update unit tests + vignette.

neurogenomics · May 9, 2024 · 91bb8d1 · 91bb8d1
1 parent c6a7a79
commit 91bb8d1
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Showing 8 changed files with 19 additions and 27 deletions.
diff --git a/R/read_motif_file.R b/R/read_motif_file.R
@@ -37,7 +37,7 @@ read_motif_file <- function(motif_file,
   )
 
   if (!file_format %in% names(read_functions)) {
-    stop(
+    stopper(
       "Unsupported file format. The motif file must be one of",
       "homer, jaspar, meme, transfac or uniprobe."
     )

diff --git a/tests/testthat/test-check_peak_input.R b/tests/testthat/test-check_peak_input.R
@@ -9,9 +9,9 @@ test_that("fail when peaks are incorrectly formatted", {
 })
 
 test_that("list outputted by check_peak_input function", {
-  data("creb_peaks", package = "MotifStats")
+  data("ctcf_peaks", package = "MotifStats")
   res <- check_peak_input(
-    creb_peaks,
+    ctcf_peaks,
     genome_build = BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
   )
 

diff --git a/tests/testthat/test-density_plot.R b/tests/testthat/test-density_plot.R
@@ -1,12 +1,12 @@
 test_that("the density_plot function outputs a ggplot", {
   temp_dir <- withr::local_tempdir()
 
-  data("creb_peaks", package = "MotifStats")
-  data("creb_motif", package = "MotifStats")
+  data("ctcf_peaks", package = "MotifStats")
+  data("ctcf_motif", package = "MotifStats")
 
   summit_to_motif_out <- summit_to_motif(
-    peak_input = creb_peaks,
-    motif = creb_motif,
+    peak_input = ctcf_peaks,
+    motif = ctcf_motif,
     fp_rate = 0.05,
     out_dir = temp_dir,
     genome_build = BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38

diff --git a/tests/testthat/test-markov_background_model.R b/tests/testthat/test-markov_background_model.R
@@ -1,10 +1,10 @@
 test_that("file created by markov_background_model function", {
   temp_dir <- withr::local_tempdir()
 
-  data("creb_peaks", package = "MotifStats")
+  data("ctcf_peaks", package = "MotifStats")
   genome_build <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
   peak_sequences <- BSgenome::getSeq(genome_build,
-                                     creb_peaks)
+                                     ctcf_peaks)
 
   res <- markov_background_model(sequences = peak_sequences,
                                  out_dir = temp_dir)

diff --git a/tests/testthat/test-motif_enrichment.R b/tests/testthat/test-motif_enrichment.R
@@ -1,13 +1,13 @@
 test_that("list outputted by motif_enrichment function", {
-  data("creb_peaks", package = "MotifStats")
-  data("creb_motif", package = "MotifStats")
+  data("ctcf_peaks", package = "MotifStats")
+  data("ctcf_motif", package = "MotifStats")
 
   temp_dir <- withr::local_tempdir()
   withr::defer(temp_dir)
 
   res <- motif_enrichment(
-    peak_input = creb_peaks,
-    motif = creb_motif,
+    peak_input = ctcf_peaks,
+    motif = ctcf_motif,
     genome_build = BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38,
     out_dir = temp_dir
     )

diff --git a/tests/testthat/test-read_peak_file.R b/tests/testthat/test-read_peak_file.R
@@ -1,6 +1,6 @@
 test_that("The output of read_peak_file is a GRanges object", {
   peak_file <- system.file("extdata",
-                           "creb_subset.narrowPeak",
+                           "ctcf_subset.narrowPeak",
                            package = "MotifStats")
   res <- read_peak_file(file_path = peak_file)
 

diff --git a/tests/testthat/test-summit_to_motif.R b/tests/testthat/test-summit_to_motif.R
@@ -1,12 +1,12 @@
 test_that("list outputted by summit_to_motif function", {
   temp_dir <- withr::local_tempdir()
 
-  data("creb_peaks", package = "MotifStats")
-  data("creb_motif", package = "MotifStats")
+  data("ctcf_peaks", package = "MotifStats")
+  data("ctcf_motif", package = "MotifStats")
 
   res <- summit_to_motif(
-    peak_input = creb_peaks,
-    motif = creb_motif,
+    peak_input = ctcf_peaks,
+    motif = ctcf_motif,
     fp_rate = 5e-02,
     genome_build = BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38,
     out_dir = temp_dir

diff --git a/vignettes/MotifStats.Rmd b/vignettes/MotifStats.Rmd
@@ -36,18 +36,11 @@ is used to recover the locations of each motif.
 The `MotifStats` package comes with motif and peak data for transcription
 factors CTCF and CREB1. Details of the files are as follows:
 
-- **CREB1 TIP-seq peaks (narrowPeaks)**[^f1]
--- *Data not publicly available*  
-
 - **CTCF TIP-seq peaks (narrowPeaks)**[^f1]
 -- Retrieved from NCBI GEO under
 accession
 [GSE188512](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE188512)  
 
-- **CREB motif**
--- Retrieved from JASPAR2024 under matrix ID
-[MA0018.5](http://jaspar.genereg.net/matrix/MA0018.5/)  
-
 - **CTCF motif**
 -- Retrieved from JASPAR2024 under matrix ID
 [MA1930.2](http://jaspar.genereg.net/matrix/MA1930.2/)  
@@ -210,8 +203,7 @@ sessionInfo()
 
 
 <!-- Footnotes -->
-[^f1]: The peak file is a subset of chromosome 19 to reduce the size of the
-built-in data.
+[^f1]: The peak file is a subset of chromosome 19 to reduce the file size.
 [^f2]: narrowPeak files from both version 2 and 3 of [MACS: Model-based Analysis
 for ChIP-Seq](https://github.com/macs3-project/MACS) is supported.
 [^f3]: For more information on the output files, refer to the