Devel

.Rbuildignore

@@ -0,0 +1,15 @@
+^LICENSE\.md$
+^README\.Rmd$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^\.github$
+^doc$
+^Meta$
+(^|/)\._
+(^|/)\.DS_Store$
+^\.Rhistory$
+^\.RData$
+^\.Ruserdata$
+^\.Rproj\.user$
+^\.github

.github/.gitignore

@@ -1,2 +1,2 @@
 *.html
-/icbb/projects/igunduz/methylTFR/.github/workflows/check-bioc.yml
+/icbb/projects/igunduz/methylTFRAnnotationHg38/.github/workflows/check-bioc.yml

DESCRIPTION

@@ -15,7 +15,7 @@ Authors@R: person(
            comment = c(ORCID = "0000-0003-2641-0916"))
 License: Artistic-2.0
 Encoding: UTF-8
-Version: 0.99.2
+Version: 0.99.6
 Depends: R (>= 4.3.0)
 Imports: AnnotationHub, GenomicRanges, utils
 Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle

NEWS.md

@@ -1,4 +1,4 @@
-# methylTFRAnnotationHg38 0.99.0
+# methylTFRAnnotationHg38 0.99.6
 
 * Initial submission to Bioconductor.
 
@@ -12,4 +12,8 @@
 * The genome-wide GC table uses non-overlapping 30 nt windows binned
   into five genome-wide GC quintiles. Bin boundaries are recorded with
   the object so that the motif frequency tables and the genome table
-  are always binned on the same scale.
+  are always binned on the same scale.
+
+* Fixes on NOTES from biocchecks
+
+* Added 4 spaces as suggested

R/aaa-utils.R

@@ -1,5 +1,3 @@
-#' @noRd
-.local_dir <- function() { ... }
 .PKG_NAME <- "methylTFRAnnotationHg38"
 .MOTIF_SETS <- c("altius", "cisbpv2", "jaspar2020", "jaspar2020_distal")
 .ASSEMBLY <- "hg38"
@@ -51,8 +49,10 @@
 .check_motif_set <- function(motifSet) {
     motifSet <- tolower(motifSet)
     if (length(motifSet) != 1 || !motifSet %in% .MOTIF_SETS) {
-        stop("Invalid motif set. Available: ",
-            paste(.MOTIF_SETS, collapse = ", "))
+        stop(
+            "Invalid motif set. Available: ",
+            paste(.MOTIF_SETS, collapse = ", ")
+        )
     }
     motifSet
 }

R/getGCfreq.R

@@ -1,30 +1,32 @@
 #' @title getGCfreq
-#' @description Load the motif GC frequency table for a motif set. Downloaded from AnnotationHub on first use and cached locally thereafter.
-#' @param motifSet Motif set to load. One of: altius, cisbpv2, jaspar2020, jaspar2020_distal.
+#' @description Load the motif GC frequency table for a motif set.
+#' Downloaded from AnnotationHub on first use and cached locally thereafter.
+#' @param motifSet Motif set to load. One of: altius, cisbpv2, jaspar2020,
+#' jaspar2020_distal.
 #' @return A named \code{list} of five-row matrices, one per motif.
 #' @examples
-#' # 1. Create a dummy object and save it to a temporary directory 
+#' # 1. Create a dummy object and save it to a temporary directory
 #' # to bypass AnnotationHub during package checks.
 #' mock_dir <- tempdir()
 #' mock_file <- file.path(mock_dir, "altius_motif_gcfreq.rds")
-#' 
+#'
 #' # (Mocking a 5-row matrix as expected by the function output)
 #' mock_data <- list(mock_motif_1 = matrix(0.25, nrow = 5, ncol = 4))
 #' saveRDS(mock_data, mock_file)
-#' 
+#'
 #' # 2. Temporarily point the package's local directory to tempdir()
 #' old_opt <- getOption("methylTFRAnnotationHg38.datadir")
 #' options(methylTFRAnnotationHg38.datadir = mock_dir)
-#' 
+#'
 #' # 3. Run the function (it will now read the mock file)
 #' x <- getGCfreq(motifSet = "altius")
-#' 
+#'
 #' # 4. Restore options and clean up the temporary file
 #' options(methylTFRAnnotationHg38.datadir = old_opt)
 #' file.remove(mock_file)
-#' 
+#'
 #' @export
 getGCfreq <- function(motifSet = "altius") {
     motifSet <- .check_motif_set(motifSet)
     .resolve_resource(paste0(motifSet, "_motif_gcfreq.rds"))
-}
+}

R/getGenomeGC.R

@@ -11,26 +11,26 @@
 #' # 1. Create a dummy object and save it to a temp directory
 #' mock_dir <- tempdir()
 #' mock_file <- file.path(mock_dir, "genomewide_GC_hg38.rds")
-#' 
+#'
 #' # Mocking a GRanges object with the expected metadata columns
 #' mock_gr <- GenomicRanges::GRanges("chr1:1-100")
 #' mock_gr$GC_bias <- 0.5
 #' mock_gr$GC_bin <- 1L
 #' saveRDS(mock_gr, mock_file)
-#' 
+#'
 #' # 2. Point the local directory option to the temp directory
 #' old_opt <- getOption("methylTFRAnnotationHg38.datadir")
 #' options(methylTFRAnnotationHg38.datadir = mock_dir)
-#' 
+#'
 #' # 3. Run the function
 #' gc <- getGenomeGC()
-#' 
+#'
 #' # 4. Restore options and clean up
 #' options(methylTFRAnnotationHg38.datadir = old_opt)
 #' file.remove(mock_file)
-#' 
+#'
 #' @export
 getGenomeGC <- function(assembly = .ASSEMBLY) {
     assembly <- tolower(assembly)
     .resolve_resource(paste0("genomewide_GC_", assembly, ".rds"))
-}
+}

R/getTFbindsites.R

@@ -1,32 +1,34 @@
 #' @title getTFbindsites
-#' @description Retrieve transcription factor binding sites for a motif set. Downloaded from AnnotationHub on first use and cached locally thereafter.
-#' @param motifSet Motif set to load. One of: altius, cisbpv2, jaspar2020, jaspar2020_distal.
+#' @description Retrieve transcription factor binding sites for a motif set.
+#' Downloaded from AnnotationHub on first use and cached locally thereafter.
+#' @param motifSet Motif set to load. One of: altius, cisbpv2, jaspar2020,
+#' jaspar2020_distal.
 #' @return A \code{GRangesList}, one element per motif.
 #' @import GenomicRanges
 #' @examples
 #' # 1. Create a dummy object and save it to a temp directory
 #' mock_dir <- tempdir()
 #' mock_file <- file.path(mock_dir, "altius_tf_bindsites.rds")
-#' 
+#'
 #' # Mocking a GRangesList as expected by the function output
 #' mock_grl <- GenomicRanges::GRangesList(
 #'     mock_motif_1 = GenomicRanges::GRanges("chr1:100-200")
 #' )
 #' saveRDS(mock_grl, mock_file)
-#' 
+#'
 #' # 2. Point the local directory option to the temp directory
 #' old_opt <- getOption("methylTFRAnnotationHg38.datadir")
 #' options(methylTFRAnnotationHg38.datadir = mock_dir)
-#' 
+#'
 #' # 3. Run the function
 #' x <- getTFbindsites()
-#' 
+#'
 #' # 4. Restore options and clean up
 #' options(methylTFRAnnotationHg38.datadir = old_opt)
 #' file.remove(mock_file)
-#' 
+#'
 #' @export
 getTFbindsites <- function(motifSet = "altius") {
     motifSet <- .check_motif_set(motifSet)
     .resolve_resource(paste0(motifSet, "_tf_bindsites.rds"))
-}
+}

tests/testthat/test-accessors.R

@@ -11,6 +11,7 @@ test_that("metadata.csv covers every declared motif set", {
     md <- utils::read.csv(system.file("extdata", "metadata.csv", package = "methylTFRAnnotationHg38"))
     for (s in methylTFRAnnotationHg38:::.MOTIF_SETS) {
         expect_true(any(grepl(paste0("^", s, "_"), md$Title)),
-            info = s)
+            info = s
+        )
     }
 })

vignettes/methylTFRAnnotationHg38.Rmd

@@ -7,7 +7,7 @@ vignette: >
   %\VignetteEncoding{UTF-8}
 ---
 
-```{r, include = FALSE}
+```{r setup, include = FALSE}
 knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
 ```
 
@@ -17,11 +17,11 @@ knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
 compute bias-corrected transcription factor deviation scores on hg38:
 
 - **binding sites**, one `GRanges` per motif, each range extended
-  so that methylation can be read across the footprint window;
+    so that methylation can be read across the footprint window;
 - **motif GC frequency tables**, recording how each motif's binding
-  sites distribute across genome-wide GC quintiles;
+    sites distribute across genome-wide GC quintiles;
 - **the genome-wide GC distribution**, which assigns each
-  methylation call to a GC bin.
+    methylation call to a GC bin.
 
 The GC tables are what make the deviation score bias-corrected. A
 motif whose binding sites sit in GC-rich sequence will overlap CpG
@@ -60,31 +60,34 @@ options(methylTFRAnnotationHg38.datadir = mock_dir)
 
 # Usage
 
-```{r}
+```{r usage}
 library(methylTFRAnnotationHg38)
 
 tf_bindsites <- getTFbindsites("altius")
-gcfreqs      <- getGCfreq("altius")
-gc_dist      <- getGenomeGC()
+gcfreqs <- getGCfreq("altius")
+gc_dist <- getGenomeGC()
 ```
 
 These are passed straight to `methylTFR::run_methyltfr()`.
 
 # Available motif sets
 
-```{r, eval = FALSE}
+```{r available_motifs, eval = FALSE}
 methylTFRAnnotationHg38:::.MOTIF_SETS
 ```
 
-Sets ending in `_distal` provide GC frequency tables computed over distal regulatory regions only. They share the unrestricted binding sites, so pass the base set name to `getTFbindsites()` and the `_distal` name to `getGCfreq()`.
+Sets ending in `_distal` provide GC frequency tables computed
+over distal regulatory regions only. They share the unrestricted
+binding sites, so pass the base set name to `getTFbindsites()` 
+and the `_distal` name to `getGCfreq()`.
 
 # Session info
 
-```{r}
+```{r session_info}
 sessionInfo()
 ```
 
 ```{r cleanup, include = FALSE}
 # HIDDEN CHUNK: Clean up the options
 options(methylTFRAnnotationHg38.datadir = old_opt)
-```
+```