Depends -> Imports

DESCRIPTION

@@ -7,15 +7,15 @@ Description: This package provides convenience functions for reading real-world
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
-Depends:
+Imports:
+    dplyr
     SummarizedExperiment,
     readxl,
     MultiAssayExperiment,
     tibble,
     pbapply,
     tidyr,
     purrr,
-    dplyr,
     BumpyMatrix,
     rvest,
     stringr, 

R/personalis.R

@@ -351,7 +351,12 @@ read_personalis_variant_calling_summary_statistics <- function(sample_folder, mo
 }
 
 #' Read in (unfiltered) small variant data from VCF files from personalis folders
-#' @param sample_list A vector of paths to personalis folders
+#' @param sample_paths A vector of paths to personalis folders
+#' @param sample_type Can be one or multiple of of 'tumor', 'normal', or 'somatic'.
+#'   'tumor' refers to tumor sample vs. genome reference (i.e. somatic+germline mutations),
+#'   'normal' refers to normal sample vs. genome reference (i.e. germline mutations) and
+#'   'somatic' refers to tumor vs. normal (i.e. somatic mutations only).
+#' @param modality modality from which the variants were called. Can be either 'DNA' or 'RNA'
 #' @return SummarizedExperiment
 #' @export
 read_personalis_vcf_files <- function(sample_paths, modality, sample_type) {

R/util.R

@@ -98,6 +98,7 @@ read_samples <- function(sample_paths, io_func, description, ...) {
 #' @param col_data {data.frame} data frame that is used as colData (must have rownames that are sample identifiers!)
 #' @param sample_col {character} column in `df` that contains the sample identifier
 #' @return {tibble} new data frame with dummy entries added
+#' @importFrom tibble as_tibble
 #' @keywords internal
 add_dummy_entry <- function(df, col_data, sample_col = "sample") {
   missing_samples <- setdiff(rownames(col_data), unique(df[[sample_col]]))
@@ -122,6 +123,7 @@ add_dummy_entry <- function(df, col_data, sample_col = "sample") {
 #' @importFrom dplyr mutate left_join
 #' @importFrom vcfR read.vcfR vcfR2tidy
 #' @importFrom stringr str_split_i
+#' @importFrom tibble as_tibble
 parse_vcf_to_df <- function(path) {
   # parse VCF file
   vcf_content <- read.vcfR(path)