Merge pull request #78 from umccr/devtools_fixes

Pass devtools checks
umccr · May 7, 2024 · c1cda25 · c1cda25
2 parents 14c1f5e + 327f170
commit c1cda25
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Showing 20 changed files with 311 additions and 228 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -43,8 +43,7 @@ Suggests:
     scales,
     sigrap,
     testthat (>= 3.0.0),
-    tibble,
-    tidyselect,
+    tibble
 Roxygen: list(markdown = TRUE,
               roclets = c("namespace", "rd", "roxytest::testthat_roclet"))
 biocViews:

diff --git a/R/oncokb.R b/R/oncokb.R
@@ -1,12 +1,23 @@
+#' Read OncoKB
+#'
+#' @param x Path to something.
+#'
+#' @return Vector of genes.
 #' @export
 read_oncokb <- function(x) {
   readr::read_tsv(x) |>
     dplyr::filter(
-      `OncoKB Annotated` == "Yes"
+      .data$`OncoKB Annotated` == "Yes"
     ) |>
     dplyr::pull("Hugo Symbol")
 }
 
+#' Get OncoKB Genes From Somewhere
+#'
+#' @param x Path to something.
+#' @param oncokb_genes A tibble of something.
+#' @return A vector I think.
+#'
 #' @export
 get_oncokb_genes <- function(x, oncokb_genes) {
   delimiters <- " ,&-"
@@ -16,9 +27,11 @@ get_oncokb_genes <- function(x, oncokb_genes) {
     # Create regexes for each match, utilising delimiters for boundaries. Handles most cases where a gene symbol contains the '-' delimiter
     purrr::map(function(n) paste0("(?<=^|", delimiter_re, ")", n, "(?=", delimiter_re, "|$)")) |>
     # Loop with nm iterations through regex and gene symbols
-    purrr::map(function(n) stringr::str_detect(x, n) |> tibble::as_tibble_row(.name_repair="unique_quiet")) |>
+    purrr::map(function(n) stringr::str_detect(x, n) |> tibble::as_tibble_row(.name_repair = "unique_quiet")) |>
     # Combine as tibble to access dplyr::summarise and compile list of detected OncoKB gene symbols for each effect
     dplyr::bind_rows() |>
-    dplyr::summarise(dplyr::across(dplyr::everything(), function(v) { paste0(sort(oncokb_genes[v]), collapse=", ") })) |>
+    dplyr::summarise(dplyr::across(dplyr::everything(), function(v) {
+      paste0(sort(oncokb_genes[v]), collapse = ", ")
+    })) |>
     unlist()
 }
diff --git a/R/oncoviral.R b/R/oncoviral.R
@@ -12,11 +12,10 @@
 #' x <- system.file("extdata/virusbreakend/virusbreakend.vcf.summary.tsv", package = "gpgr")
 #' (vb <- virusbreakend_summary_read(x))
 #' @testexamples
-#' expect_equal(colnames(vb)[ncol(vb)], "QCStatus")
+#' expect_equal(colnames(vb$tab)[ncol(vb$tab)], "QC")
 #'
 #' @export
 virusbreakend_summary_read <- function(x) {
-
   nm <- c(
     "taxid_genus" = "c",
     "name_genus" = "c",
@@ -44,7 +43,6 @@ virusbreakend_summary_read <- function(x) {
     "integrations" = "i",
     "QCStatus" = "c"
   )
-
   ctypes <- paste(nm, collapse = "")
   virusbreakend_summary <- readr::read_tsv(x, col_types = ctypes)
 
@@ -54,13 +52,13 @@ virusbreakend_summary_read <- function(x) {
 
     virusbreakend_summary <- virusbreakend_summary |>
       dplyr::select(
-        Virus="name_assigned",
-        Length="endpos",
-        Reads="numreads",
-        Coverage="coverage",
-        `Mean depth`="meandepth",
-        Intergrations="integrations",
-        QC="QCStatus",
+        Virus = "name_assigned",
+        Length = "endpos",
+        Reads = "numreads",
+        Coverage = "coverage",
+        `Mean depth` = "meandepth",
+        Intergrations = "integrations",
+        QC = "QCStatus",
       )
   }
 
@@ -71,7 +69,7 @@ virusbreakend_summary_read <- function(x) {
     "Reads", "Number of reads mapped to adjusted viral reference",
     "Coverage", "Percentage of viral positions with at least one read mapped",
     "Mean depth", "Mean alignment depth",
-    "Intergrations", "Number of detected integration breakpoints",
+    "Integrations", "Number of detected integration breakpoints",
     "QC", "QC status of viral intergrations",
   )
 
@@ -95,29 +93,28 @@ virusbreakend_summary_read <- function(x) {
 #' x <- system.file("extdata/virusbreakend/virusbreakend.vcf", package = "gpgr")
 #' (vb <- virusbreakend_vcf_read(x))
 #' @testexamples
-#' expect_equal(colnames(vb)[ncol(vb)], "QC")
+#' expect_equal(colnames(vb$tab)[ncol(vb$tab)], "QC")
 #'
 #' @export
 virusbreakend_vcf_read <- function(x) {
-
   d <- bedr::read.vcf(x, split.info = TRUE, verbose = FALSE)
 
   if (nrow(d$vcf) > 0) {
     virusbreakend_integrations <- tibble::as_tibble(d$vcf) |>
       dplyr::select(
-          Contig="CHROM",
-          Position="POS",
-          "Fragment support"="BVF",
-          "Fragment support (unmapped)"="BUM",
-          "Softclip read support"="BSC",
-          Reference="REF",
-          Alt="ALT",
-          `Breakend ID`="ID",
-          `Mate ID`="MATEID",
-          QC="FILTER",
+        Contig = "CHROM",
+        Position = "POS",
+        "Fragment support" = "BVF",
+        "Fragment support (unmapped)" = "BUM",
+        "Softclip read support" = "BSC",
+        Reference = "REF",
+        Alt = "ALT",
+        `Breakend ID` = "ID",
+        `Mate ID` = "MATEID",
+        QC = "FILTER",
       )
   } else {
-      virusbreakend_integrations <- tibble::tibble()
+    virusbreakend_integrations <- tibble::tibble()
   }
 
   descr <- dplyr::tribble(