fix notes

.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/methylTFRAnnotationMm10/.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: 0.99.4
+Version: 0.99.6
 Depends: R (>= 4.3.0)
 Imports: AnnotationHub, GenomicRanges, utils
 Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle

NEWS.md

@@ -1,3 +1,18 @@
-# methylTFRAnnotationsMm10 0.99.4
+# methylTFRAnnotationMm10 0.99.6
 
-- Fix some notes found in bioccheck
+* Initial submission to Bioconductor.
+
+* Provides transcription factor binding sites, motif GC frequency
+  tables and a genome-wide GC distribution for hg38, for the
+  jaspar2020, cisbpv2 and altius motif sets GC frequency tables.
+
+* Resources are hosted on AnnotationHub and downloaded on first use.
+
+* 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.
+
+* Fixes on NOTES from biocchecks
+
+* Added 4 spaces as suggested

R/aaa-utils.R

@@ -1,18 +1,14 @@
-#' @noRd
-.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
@@ -24,39 +20,39 @@
 #' 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)"
-      )
+    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))
     }
-    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]]]
+    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

@@ -29,6 +29,6 @@
 #'
 #' @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

@@ -31,6 +31,6 @@
 #'
 #' @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

@@ -13,7 +13,7 @@
 #'
 #' # 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)
 #'
@@ -30,6 +30,6 @@
 #'
 #' @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

@@ -1,17 +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

@@ -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"))