fixy fixy fix

DESCRIPTION

@@ -14,6 +14,7 @@ BugReports: https://github.com/dynverse/dynnormaliser/issues
 Depends:
   R (>= 3.0.0)
 Imports: 
-  Matrix
+  Matrix,
+  methods
 Suggests:
   testthat

NAMESPACE

@@ -1,18 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
 export(normalise_filter_counts)
-import(dplyr)
-import(ggplot2)
-import(tibble)
-import(tidyr)
-importFrom(magrittr,"%$%")
-importFrom(magrittr,"%<>%")
-importFrom(purrr,"%>%")
-importFrom(purrr,keep)
-importFrom(purrr,map)
-importFrom(purrr,map_chr)
-importFrom(purrr,map_dbl)
-importFrom(purrr,map_df)
-importFrom(purrr,map_int)
-importFrom(purrr,map_lgl)
-importFrom(purrr,set_names)
+import(Matrix)
+importFrom(methods,as)

R/normalisation.R

@@ -1,9 +1,13 @@
 #' Normalisation
 #'
 #' @param counts The counts matrix, with features in columns
+#' @import Matrix
 #' @export
 normalise_filter_counts <- function(
   counts
 ) {
-  as(log2(counts + 1), "dgCMatrix")
+  list(
+    counts = counts,
+    expression = as(log2(counts + 1), "dgCMatrix")
+  )
 }

R/package.R

@@ -1,12 +1,8 @@
-#' Helper functions
+#' Helper functions for normalisation
 #'
-#' @import dplyr
-#' @import tidyr
-#' @import tibble
-#' @import ggplot2
-#' @importFrom purrr %>% map map_df map_chr map_lgl map_int map_dbl keep set_names
-#' @importFrom magrittr %<>% %$%
+#' Normalisation
 #'
 #' @docType package
 #' @name dynnormaliser
+#' @importFrom methods as
 NULL

tests/testthat/test-normalisation.R

@@ -18,14 +18,7 @@ test_that("Testing normalise function", {
   sink(tmpfile)
   pdf(tmpfile)
   normd <- normalise_filter_counts(
-    counts = counts,
-    verbose = TRUE,
-    nmads = 3,
-    min_ave_expression = 0.05,
-    filter_hvg = TRUE,
-    hvg_fdr = 0.05,
-    hvg_bio = 0.5,
-    min_variable_fraction = 0.1
+    counts = counts
   )
   dev.off()
   sink()
@@ -51,14 +44,7 @@ test_that("Also test for when there are no Mt genes", {
   sink(tmpfile)
   pdf(tmpfile)
   normd <- normalise_filter_counts(
-    counts = counts,
-    verbose = TRUE,
-    nmads = 3,
-    min_ave_expression = 0.05,
-    filter_hvg = TRUE,
-    hvg_fdr = 0.05,
-    hvg_bio = 0.5,
-    min_variable_fraction = 0.1
+    counts = counts
   )
   dev.off()
   sink()