diff --git a/DESCRIPTION b/DESCRIPTION
index 331e42e..4092f2e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -53,5 +53,5 @@ Suggests:
testthat (>= 3.0.0),
tidyr,
tidyverse
-VignetteBuilder: knitr
+# VignetteBuilder: knitr
Config/testthat/edition: 3
diff --git a/R/ClonalDefinition.R b/R/ClonalDefinition.R
index 5de1a9b..30df9d0 100644
--- a/R/ClonalDefinition.R
+++ b/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]],
diff --git a/R/LoadingMAEGATK_typewise.R b/R/LoadingMAEGATK_typewise.R
index 150886c..d43a878 100644
--- a/R/LoadingMAEGATK_typewise.R
+++ b/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, "."))
diff --git a/_pkgdown.yml b/_pkgdown.yml
index fb62923..038cd27 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -3,3 +3,5 @@ template:
bootstrap: 5
vignettes:
build: false
+build:
+ copy_vignettes: true
diff --git a/docs/404.html b/docs/404.html
index 7114001..28b326d 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -24,7 +24,7 @@
sigurd
- 0.2.61
+ 0.3.0