Devel

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: 0.99.4
 Depends: R (>= 4.3.0)
 Imports: AnnotationHub, GenomicRanges, utils
 Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle

NEWS.md

@@ -0,0 +1,3 @@
+# methylTFRAnnotationsMm10 0.99.4
+
+- Fix some notes found in bioccheck

R/aaa-utils.R

@@ -1,16 +1,18 @@
 #' @noRd
-.local_dir <- function() { ... }
+.local_dir <- function() {
+  ...
+}
 .PKG_NAME <- "methylTFRAnnotationMm10"
 .MOTIF_SETS <- c("altius", "cisbpv2", "jaspar2020")
 .ASSEMBLY <- "Mm10"
 
 #' @keywords internal
 .local_dir <- function() {
-    d <- getOption(
-        "methylTFRAnnotationMm10.datadir",
-        Sys.getenv("METHYL_TFRANNOTATION_Mm10_DIR", "")
-    )
-    if (nzchar(d)) d else NULL
+  d <- getOption(
+    "methylTFRAnnotationMm10.datadir",
+    Sys.getenv("METHYL_TFRANNOTATION_Mm10_DIR", "")
+  )
+  if (nzchar(d)) d else NULL
 }
 
 #' @keywords internal
@@ -22,37 +24,39 @@
 #' on the hub, and so users who have downloaded the files by hand
 #' can point at them.
 .resolve_resource <- function(file) {
-    dir <- .local_dir()
-    if (!is.null(dir)) {
-        path <- file.path(dir, file)
-        if (!file.exists(path)) {
-            stop(
-                "Annotation file not found: ", path,
-                "\n(reading from a local directory because ",
-                .PKG_NAME, ".datadir is set)"
-            )
-        }
-        return(readRDS(path))
-    }
-    hub <- AnnotationHub::AnnotationHub()
-    hits <- AnnotationHub::query(hub, .PKG_NAME)
-    idx <- match(file, hits$title)
-    if (is.na(idx)) {
-        stop(
-            "Resource not found on AnnotationHub: ", file,
-            "\nAvailable: ", paste(hits$title, collapse = ", ")
-        )
+  dir <- .local_dir()
+  if (!is.null(dir)) {
+    path <- file.path(dir, file)
+    if (!file.exists(path)) {
+      stop(
+        "Annotation file not found: ", path,
+        "\n(reading from a local directory because ",
+        .PKG_NAME, ".datadir is set)"
+      )
     }
-    hits[[names(hits)[idx]]]
+    return(readRDS(path))
+  }
+  hub <- AnnotationHub::AnnotationHub()
+  hits <- AnnotationHub::query(hub, .PKG_NAME)
+  idx <- match(file, hits$title)
+  if (is.na(idx)) {
+    stop(
+      "Resource not found on AnnotationHub: ", file,
+      "\nAvailable: ", paste(hits$title, collapse = ", ")
+    )
+  }
+  hits[[names(hits)[idx]]]
 }
 
 #' @keywords internal
 #' @noRd
 .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 = ", "))
-    }
-    motifSet
+  motifSet <- tolower(motifSet)
+  if (length(motifSet) != 1 || !motifSet %in% .MOTIF_SETS) {
+    stop(
+      "Invalid motif set. Available: ",
+      paste(.MOTIF_SETS, collapse = ", ")
+    )
+  }
+  motifSet
 }

R/getGCfreq.R

@@ -1,32 +1,34 @@
 #' @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.
 #' @import GenomicRanges
 #' @importFrom utils packageVersion
 #' @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("methylTFRAnnotationMm10.datadir")
 #' options(methylTFRAnnotationMm10.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(methylTFRAnnotationMm10.datadir = old_opt)
 #' file.remove(mock_file)
-#' 
+#'
 #' @export
 getGCfreq <- function(motifSet = "altius") {
-    motifSet <- .check_motif_set(motifSet)
-    .resolve_resource(paste0(motifSet, "_motif_gcfreq.rds"))
+  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 temporary directory
 #' mock_dir <- tempdir()
 #' mock_file <- file.path(mock_dir, "genomewide_GC_mm10.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. Temporarily point the package to tempdir
 #' old_opt <- getOption("methylTFRAnnotationMm10.datadir")
 #' options(methylTFRAnnotationMm10.datadir = mock_dir)
-#' 
+#'
 #' # 3. Run the function
 #' gc <- getGenomeGC()
-#' 
+#'
 #' # 4. Restore options and clean up
 #' options(methylTFRAnnotationMm10.datadir = old_opt)
 #' file.remove(mock_file)
-#' 
+#'
 #' @export
 getGenomeGC <- function(assembly = .ASSEMBLY) {
-    assembly <- tolower(assembly)
-    .resolve_resource(paste0("genomewide_GC_", assembly, ".rds"))
-}
+  assembly <- tolower(assembly)
+  .resolve_resource(paste0("genomewide_GC_", assembly, ".rds"))
+}

R/getTFbindsites.R

@@ -1,33 +1,35 @@
 #' @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
 #' @importFrom utils packageVersion
 #' @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")
+#'   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("methylTFRAnnotationMm10.datadir")
 #' options(methylTFRAnnotationMm10.datadir = mock_dir)
-#' 
+#'
 #' # 3. Run the function
 #' x <- getTFbindsites()
-#' 
+#'
 #' # 4. Restore options and clean up
 #' options(methylTFRAnnotationMm10.datadir = old_opt)
 #' file.remove(mock_file)
-#' 
+#'
 #' @export
 getTFbindsites <- function(motifSet = "altius") {
-    motifSet <- .check_motif_set(motifSet)
-    .resolve_resource(paste0(motifSet, "_tf_bindsites.rds"))
+  motifSet <- .check_motif_set(motifSet)
+  .resolve_resource(paste0(motifSet, "_tf_bindsites.rds"))
 }

tests/testthat/test-accessors.R

@@ -1,16 +1,17 @@
 test_that("motif set validation rejects unknown sets", {
-    expect_error(getGCfreq("not_a_motif_set"), "Invalid motif set")
-    expect_error(getGCfreq(c("a", "b")), "Invalid motif set")
+  expect_error(getGCfreq("not_a_motif_set"), "Invalid motif set")
+  expect_error(getGCfreq(c("a", "b")), "Invalid motif set")
 })
 
 test_that("motif set validation is case insensitive", {
-    expect_identical(methylTFRAnnotationMm10:::.check_motif_set("ALTIUS"), "altius")
+  expect_identical(methylTFRAnnotationMm10:::.check_motif_set("ALTIUS"), "altius")
 })
 
 test_that("metadata.csv covers every declared motif set", {
-    md <- utils::read.csv(system.file("extdata", "metadata.csv", package = "methylTFRAnnotationMm10"))
-    for (s in methylTFRAnnotationMm10:::.MOTIF_SETS) {
-        expect_true(any(grepl(paste0("^", s, "_"), md$Title)),
-            info = s)
-    }
+  md <- utils::read.csv(system.file("extdata", "metadata.csv", package = "methylTFRAnnotationMm10"))
+  for (s in methylTFRAnnotationMm10:::.MOTIF_SETS) {
+    expect_true(any(grepl(paste0("^", s, "_"), md$Title)),
+      info = s
+    )
+  }
 })

vignettes/methylTFRAnnotationMm10.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 Mm10:
 
 - **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
@@ -30,8 +30,8 @@ hypomethylated; without the correction that difference in sequence
 composition would read as a difference in factor activity.
 
 The data are too large to ship inside the package, so they are
-hosted on AnnotationHub and downloaded on first use. Subsequent
-calls are served from the local AnnotationHub cache.
+hosted on `AnnotationHub` and downloaded on first use. Subsequent
+calls are served from the local `AnnotationHub` cache.
 
 
 ```{r dummy, include = FALSE}
@@ -40,7 +40,7 @@ mock_dir <- tempdir()
 
 # 1. Mock TF bindsites
 mock_grl <- GenomicRanges::GRangesList(
-    mock_motif_1 = GenomicRanges::GRanges("chr1:100-200")
+  mock_motif_1 = GenomicRanges::GRanges("chr1:100-200")
 )
 saveRDS(mock_grl, file.path(mock_dir, "altius_tf_bindsites.rds"))
 
@@ -61,30 +61,30 @@ options(methylTFRAnnotationMm10.datadir = mock_dir)
 
 # Usage
 
-```{r, eval = FALSE}
+```{r usage, eval = FALSE}
 library(methylTFRAnnotationMm10)
 
 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}
 methylTFRAnnotationMm10:::.MOTIF_SETS
 ```
 
 # Session info
 
-```{r}
+```{r session_info}
 sessionInfo()
 ```
 
 
 ```{r cleanup, include = FALSE}
 # HIDDEN CHUNK: Clean up the options
 options(methylTFRAnnotationMm10.datadir = old_opt)
-```
+```