Devel

CITATION.cff

@@ -12,8 +12,8 @@ authors:
     given-names: Irem B.
     email: irembgunduz@gmail.com
     orcid: "https://orcid.org/0000-0003-2641-0916"
-version: 0.99.10
-date-released: "2026-09-29"
+version: 0.99.12
+date-released: "2026-10-02"
 doi: 10.18129/B9.bioc.methylTFRAnnotationMm10
 license: Artistic-2.0
 repository-code: "https://github.com/EpigenomeInformatics/methylTFRAnnotationMm10"

DESCRIPTION

@@ -19,8 +19,8 @@ Authors@R: c(
   )
 License: Artistic-2.0
 Encoding: UTF-8
-Version: 0.99.10
-Depends: R (>= 4.3.0)
+Version: 0.99.12
+Depends: R (>= 4.6.0)
 Imports: AnnotationHub, GenomicRanges, stats
 Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle
 VignetteBuilder: knitr

NEWS.md

@@ -1,3 +1,25 @@
+# methylTFRAnnotationMm10 0.99.12
+
+Changes in response to the second review:
+
+* Depends on R (>= 4.6.0).
+* Input checking: an invalid `methylTFRAnnotationMm10.datadir` option or
+  `METHYL_TFRANNOTATION_Mm10_DIR` value (not a single string, or a directory
+  that does not exist) now gives an informative error. Tests
+  added.
+* Added `inst/extdata/README.md` describing `metadata.csv` and
+  each AnnotationHub resource.
+* The vignette's Installation section also installs methylTFR.
+
+# methylTFRAnnotationMm10 0.99.11
+
+* BiocCheck fixes: the data help pages (`?motif_gcfreq`,
+  `?tf_bindsites`, `?genomewide_GC`) have a `\value` section, and
+  their examples run (reading `metadata.csv`) instead of using
+  `\dontrun`.
+* Shortened vignette lines to at most 80 characters.
+* Added `CITATION.cff`.
+
 # methylTFRAnnotationMm10 0.99.10
 
 Changes in response to the Bioconductor review:

R/aaa-utils.R

@@ -9,7 +9,24 @@
         "methylTFRAnnotationMm10.datadir",
         Sys.getenv("METHYL_TFRANNOTATION_Mm10_DIR", "")
     )
-    if (is.character(d) && length(d) == 1L && nzchar(d)) d else NULL
+    if (is.null(d) || identical(d, "")) {
+        return(NULL)
+    }
+    if (!is.character(d) || length(d) != 1L || is.na(d)) {
+        stop(
+            "The option methylTFRAnnotationMm10.datadir must be a single ",
+            "character string (a directory path)."
+        )
+    }
+    if (!dir.exists(d)) {
+        stop(
+            "Local annotation directory does not exist: ", d,
+            "\nUnset options(methylTFRAnnotationMm10.datadir) and the ",
+            "METHYL_TFRANNOTATION_Mm10_DIR environment variable ",
+            "to use AnnotationHub."
+        )
+    }
+    d
 }
 
 #' @keywords internal

R/resources.R

@@ -42,14 +42,18 @@
 #' and \code{system.file("extdata", "metadata.csv", package =
 #' "methylTFRAnnotationMm10")} for the exact sources and versions.
 #' @seealso \code{\link{getGCfreq}}, \code{\link{methylTFRAnnotationMm10}}
+#' @return This page documents a data resource rather than a
+#' function; the object is returned by \code{\link{getGCfreq}}.
 #' @examples
-#' ## On first use this downloads the resource from AnnotationHub:
-#' \dontrun{
-#' gcfreqs <- getGCfreq("jaspar2020")
-#' length(gcfreqs)          # number of motifs
-#' dim(gcfreqs[[1]])        # 5 x number of window positions
-#' colSums(gcfreqs[[1]])    # all 1
-#' }
+#' # AnnotationHub records of this resource and their descriptions
+#' md <- utils::read.csv(system.file("extdata", "metadata.csv",
+#'     package = "methylTFRAnnotationMm10"
+#' ))
+#' md[grepl("_motif_gcfreq", md$Title), c("Title", "RDataClass")]
+#'
+#' # Loading the resource downloads it from AnnotationHub on first use:
+#' # gcfreqs <- getGCfreq("jaspar2020")
+#' # length(gcfreqs); dim(gcfreqs[[1]]); colSums(gcfreqs[[1]])
 #' @keywords datasets
 NULL
 
@@ -75,14 +79,18 @@ NULL
 #' }
 #' @source See \code{\link{motif_gcfreq}}.
 #' @seealso \code{\link{getTFbindsites}}, \code{\link{methylTFRAnnotationMm10}}
+#' @return This page documents a data resource rather than a
+#' function; the object is returned by \code{\link{getTFbindsites}}.
 #' @examples
-#' ## On first use this downloads the resource from AnnotationHub:
-#' \dontrun{
-#' tfbs <- getTFbindsites("jaspar2020")
-#' length(tfbs)                 # number of motifs
-#' head(lengths(tfbs))          # binding sites per motif
-#' tfbs[[1]]
-#' }
+#' # AnnotationHub records of this resource and their descriptions
+#' md <- utils::read.csv(system.file("extdata", "metadata.csv",
+#'     package = "methylTFRAnnotationMm10"
+#' ))
+#' md[grepl("_tf_bindsites", md$Title), c("Title", "RDataClass")]
+#'
+#' # Loading the resource downloads it from AnnotationHub on first use:
+#' # tfbs <- getTFbindsites("jaspar2020")
+#' # length(tfbs); head(lengths(tfbs)); tfbs[[1]]
 #' @keywords datasets
 NULL
 
@@ -110,13 +118,17 @@ NULL
 #' \code{system.file("scripts", "make-data.R", package =
 #' "methylTFRAnnotationMm10")}.
 #' @seealso \code{\link{getGenomeGC}}, \code{\link{methylTFRAnnotationMm10}}
+#' @return This page documents a data resource rather than a
+#' function; the object is returned by \code{\link{getGenomeGC}}.
 #' @examples
-#' ## On first use this downloads the resource from AnnotationHub:
-#' \dontrun{
-#' gc <- getGenomeGC()
-#' gc
-#' table(gc$GC_bin)
-#' S4Vectors::metadata(gc)$gc_breaks
-#' }
+#' # AnnotationHub records of this resource and their descriptions
+#' md <- utils::read.csv(system.file("extdata", "metadata.csv",
+#'     package = "methylTFRAnnotationMm10"
+#' ))
+#' md[grepl("genomewide_GC", md$Title), c("Title", "RDataClass")]
+#'
+#' # Loading the resource downloads it from AnnotationHub on first use:
+#' # gc <- getGenomeGC()
+#' # table(gc$GC_bin); S4Vectors::metadata(gc)$gc_breaks
 #' @keywords datasets
 NULL

inst/extdata/README.md

@@ -0,0 +1,55 @@
+# methylTFRAnnotationMm10: `inst/extdata`
+
+This directory contains `metadata.csv`, the AnnotationHub metadata for
+the resources served by methylTFRAnnotationMm10. The data files themselves
+are hosted on AnnotationHub (they are too large to ship with the
+package) and are downloaded on first use by the accessor functions.
+
+## Resources
+
+| Title | R class | Accessor | Help page |
+|---|---|---|---|
+| `altius_motif_gcfreq.rds` | `list` | `getGCfreq("altius")` | `?motif_gcfreq` |
+| `altius_tf_bindsites.rds` | `GRangesList` | `getTFbindsites("altius")` | `?tf_bindsites` |
+| `cisbpv2_motif_gcfreq.rds` | `list` | `getGCfreq("cisbpv2")` | `?motif_gcfreq` |
+| `cisbpv2_tf_bindsites.rds` | `GRangesList` | `getTFbindsites("cisbpv2")` | `?tf_bindsites` |
+| `genomewide_GC_mm10.rds` | `GRanges` | `getGenomeGC()` | `?genomewide_GC` |
+| `jaspar2020_motif_gcfreq.rds` | `list` | `getGCfreq("jaspar2020")` | `?motif_gcfreq` |
+| `jaspar2020_tf_bindsites.rds` | `GRangesList` | `getTFbindsites("jaspar2020")` | `?tf_bindsites` |
+
+* `<set>_tf_bindsites.rds`: genome-wide motif matches for one motif set,
+  one `GRanges` per motif, each range extended by 200 bp on either side
+  of the match.
+* `<set>_motif_gcfreq.rds`: one 5 x n numeric matrix per motif. Rows are
+  genome-wide GC quintiles (lowest first), columns are positions of a
+  30 nt window along the binding site; each column gives the fraction of
+  the motif's sites in each quintile and sums to one.
+* `genomewide_GC_mm10.rds`: non-overlapping 30 nt windows across the
+  primary chromosomes with their GC fraction (`GC_bias`) and quintile
+  (`GC_bin`); the quintile boundaries are stored in the object's metadata.
+
+## Columns of `metadata.csv`
+
+| Column | Meaning |
+|---|---|
+| `Title` | Resource name; also the file name on AnnotationHub |
+| `Description` | What the resource contains |
+| `BiocVersion` | Bioconductor version the resource was added in |
+| `Genome` | Genome assembly (`mm10`) |
+| `SourceType` | Format of the source file (`RDS`) |
+| `SourceUrl` | Where the input data (motifs, genome) come from |
+| `SourceVersion` | Version of the motif collection or genome |
+| `Species`, `TaxonomyId` | Organism and NCBI taxonomy ID |
+| `Coordinate_1_based` | Coordinates are 1-based (`TRUE`) |
+| `DataProvider` | Provider of the motif collection or genome |
+| `Maintainer` | Maintainer of the resource |
+| `RDataClass` | R class of the object (`GRangesList`, `list`, `GRanges`) |
+| `DispatchClass` | How AnnotationHub loads the file (`Rds`) |
+| `Location_Prefix`, `RDataPath` | Where the file is stored; joined, they give the download URL |
+| `Tags` | Search tags for `AnnotationHub::query()` |
+
+## How the data were made
+
+* `inst/scripts/make-data.R` builds every resource with
+  [methylTFRAnnotationBuilder](https://github.com/EpigenomeInformatics/methylTFRAnnotationBuilder).
+* `inst/scripts/make-metadata.R` writes this `metadata.csv`.

tests/testthat/test-local-resources.R

@@ -94,3 +94,16 @@ test_that("no local directory is used when neither option nor env var is set", {
     )
     expect_null(methylTFRAnnotationMm10:::.local_dir())
 })
+
+test_that("an invalid local directory setting gives an informative error", {
+    old <- options(methylTFRAnnotationMm10.datadir = c("a", "b"))
+    on.exit(options(old), add = TRUE)
+    expect_error(getGenomeGC(), "single character string")
+
+    options(methylTFRAnnotationMm10.datadir = 1)
+    expect_error(getGCfreq("altius"), "single character string")
+
+    missing_dir <- file.path(tempdir(), "does_not_exist")
+    options(methylTFRAnnotationMm10.datadir = missing_dir)
+    expect_error(getTFbindsites("altius"), "does not exist")
+})

vignettes/methylTFRAnnotationMm10.Rmd

@@ -18,9 +18,9 @@ mm10. It contains three kinds of resources, each with its own accessor:
 
 | Accessor | Returns | Help page |
 |---|---|---|
-| `getTFbindsites()` | TF binding sites, one `GRanges` per motif | `?tf_bindsites` |
-| `getGCfreq()` | motif GC frequency tables, one matrix per motif | `?motif_gcfreq` |
-| `getGenomeGC()` | genome-wide GC content in 30 nt windows | `?genomewide_GC` |
+| `getTFbindsites()` | TF binding sites (a `GRangesList`) | `?tf_bindsites` |
+| `getGCfreq()` | GC frequency tables, one per motif | `?motif_gcfreq` |
+| `getGenomeGC()` | GC content in 30 nt windows | `?genomewide_GC` |
 
 The GC tables are what make the deviation score bias-corrected. A motif
 whose binding sites sit in GC-rich sequence overlaps CpG islands more
@@ -40,6 +40,9 @@ if (!requireNamespace("BiocManager", quietly = TRUE)) {
     install.packages("BiocManager")
 }
 BiocManager::install("methylTFRAnnotationMm10")
+
+# methylTFR, which uses these annotations
+BiocManager::install("methylTFR")
 ```
 
 # Example data used in this vignette