Merge pull request #229 from sigven/pd_fixes

Various last-minute fixes

conda/recipe/pcgrr/build.sh

@@ -2,6 +2,5 @@
 
 export DISABLE_AUTOBREW=1
 ${R} -e "install.packages('remotes', repos = 'https://cloud.r-project.org/', lib = '${PREFIX}/lib/R/library')"
-${R} -e "install.packages('openxlsx2', repos = 'https://cloud.r-project.org/', lib = '${PREFIX}/lib/R/library')"
 ${R} -e "remotes::install_github(repo = 'caravagnalab/CNAqc', ref = '274cde9', lib = '${PREFIX}/lib/R/library')"
 ${R} CMD INSTALL --build . ${R_ARGS}

conda/recipe/pcgrr/meta.yaml

@@ -20,6 +20,7 @@ requirements:
     - r-assertable
     - r-assertthat
     - bioconductor-biostrings
+    - r-caret
     - r-dplyr
     - r-dt
     - r-formattable
@@ -29,6 +30,7 @@ requirements:
     - r-htmltools
     - r-log4r
     - bioconductor-mutationalpatterns
+    - r-openxlsx2
     - r-plotly
     - bioconductor-quantiseqr
     - r-quarto
@@ -49,6 +51,7 @@ requirements:
     - r-assertable
     - r-assertthat
     - bioconductor-biostrings
+    - r-caret
     - r-dplyr
     - r-dt
     - r-formattable
@@ -58,6 +61,7 @@ requirements:
     - r-htmltools
     - r-log4r
     - bioconductor-mutationalpatterns
+    - r-openxlsx2
     - r-plotly
     - bioconductor-quantiseqr
     - r-quarto

pcgrr/DESCRIPTION

@@ -30,6 +30,7 @@ Imports:
     assertable,
     assertthat,
     Biostrings,
+    caret,
     CNAqc,
     dplyr,
     DT,

pcgrr/R/cna.R

@@ -91,8 +91,7 @@ make_cnaqc_object <- function(
                     "is_driver", "driver_label"))
   }else{
     ## Make a single dummy mutation if mutations are absent
-    data('example_dataset_CNAqc', package = 'CNAqc')
-    mutations <- example_dataset_CNAqc$mutations[3,]
+    mutations <- CNAqc::example_dataset_CNAqc$mutations[3,]
   }
 
   cna <- callset_cna$variant |>

pcgrr/R/utils.R

@@ -1037,13 +1037,16 @@ mkdir <- function(d) {
 }
 
 
-# from https://github.com/yihui/xfun/blob/ccee265f74eb03b9d40d7167e8933b5c72e5892c/R/string.R#L329
-#' Strip HTML tags from a string
+#' Strip HTML tags
 #'
-#' @param x string to strip away HTML text.
+#' Remove HTML tags and comments from text.
+#' From https://github.com/yihui/xfun/blob/ccee26/R/string.R#L329.
 #'
+#' @param x A character vector.
+#' @return A character vector with HTML tags and comments stripped off.
 #' @export
-#'
+#' @examples
+#' strip_html('<a href="#">Hello <!-- comment -->world!</a>')
 strip_html <- function(x) {
     x <- gsub("<!--.*?-->", "", x)
     x <- gsub("<[^>]+>", "", x)

pcgrr/R/utils_shortcuts.R

@@ -15,4 +15,5 @@ dummy1 <- function() {
   DT::datatable
   htmltools::br
   plotly::plot_ly
+  caret::createModel
 }