Merge pull request #41 from CostaLab/devel

Fixing vignette building.

DESCRIPTION

@@ -53,5 +53,5 @@ Suggests:
     testthat (>= 3.0.0),
     tidyr,
     tidyverse
-VignetteBuilder: knitr
+# VignetteBuilder: knitr
 Config/testthat/edition: 3

R/ClonalDefinition.R

@@ -11,10 +11,11 @@
 #'@param se SummarizedExperiment object.
 #'@param variants_ls List of variants for clonal definition
 #'@param grouping The meta data	column used to split the cells into groups. Default = NULL
+#'@param n_cores Number of cores you want to use. Numeric.
 #'@param identities Vector of groups, like samples.
 #'@param verbose Should the function be verbose? Default = TRUE
 #'@export
-ClonalDefinition <- function(se, variants_ls, grouping = NULL, identities = NULL, verbose = TRUE){
+ClonalDefinition <- function(se, variants_ls, grouping = NULL, identities = NULL, n_cores = 1, verbose = TRUE){
   # Checking if the group variable is in the column data.
   if(!is.null(grouping)){
     # We check if the grouping variable is in the column data.
@@ -109,7 +110,6 @@ ClonalDefinition <- function(se, variants_ls, grouping = NULL, identities = NULL
           cells_rest <- rep(TRUE, ncol(se_use))
         }
         cells <- colSums(rbind(cells, cells_rest)) == 2
-        coverage <- mean(colMeans(SummarizedExperiment::assays(se_use)[["coverage"]][combination_use, cells, drop = FALSE]))
         cells <- cells[cells]
         new_meta_data_subset[names(cells)] <- paste0("C", combination_number)
         combinations_meta_data[[i]] <- rbind(combinations_meta_data[[i]], 

R/LoadingMAEGATK_typewise.R

@@ -26,7 +26,7 @@
 #'@param cellbarcode_length The length of the cell barcode. This should be the length of the actual barcode plus two for the suffix (-1). Default = 18
 #'@param verbose Should the function be verbose? Default = TRUE
 #'@export
-LoadingMAEGATK_typewise <- function(samples_file, samples_path = NULL, patient, patient_column = "patient", type_use = "scRNAseq_MT", chromosome_prefix = "chrM",
+LoadingMAEGATK_typewise <- function(samples_file, patient, samples_path = NULL, patient_column = "patient", type_use = "scRNAseq_MT", chromosome_prefix = "chrM",
                                     min_cells = 2, cells_include = NULL, cells_exclude = NULL, barcodes_path = NULL, cellbarcode_length = 18, verbose = TRUE){
   if(all(!is.null(samples_path), !is.null(barcodes_path))){
     if(verbose) print(paste0("Loading the data for patient ", patient, "."))

_pkgdown.yml

@@ -3,3 +3,5 @@ template:
   bootstrap: 5
 vignettes:
   build: false
+build:
+  copy_vignettes: true