Added error check if isotypes are not specified. Added NEWS

NEWS.md

@@ -1,3 +1,17 @@
+# dsb 0.2.0
+
+• Enhancements  
+quantile clipping: rarely, a small minority of cells can have outlier values for a single protein, for example expression at level -25 after normalization. These values can now be clipped to be the lowest / highest quantile by default c(0.001, 0.9995). To use this feature set `quantile.clipping = TRUE` and quantile.clip to be a vector of lowest and highest quantile values to use; by default c(0.001, 0.9995). 
+
+• return dsb internal stats  
+Some advanced users may desire to look into the latent noise variables estimated by dsb. Setting `return.stats = TRUE` now returns a list, the first element is the dsb normalized ADT values, the second element is a dataframe of noise variables for each cell, including the derived "dsb technical component" along with its constituent variables, the background mean and the isotype control protein values for each cell. 
+
+• Documentation  
+Documentation has been overhauled, the main vignette now includes simpler estimation of cells vs empty drops by using the EmptyDrops method that is now implemented by Cell Ranger by default. A workflow for multimodal (CITE-seq) single cell analysis using the dsb method for normalization is provided including loading raw data, quality control, clustering and multiple versions of the Seurat Weighted Nearest Neighbors joint mRNA and protein clustering method.  
+
+An additional vignette is provided with step by step intuition for underlying code / modeling for the dsb method. 
+
+
 # dsb 0.1.0
 
 • dsb is now hosted on CRAN: [go to dsb on CRAN](https://cran.r-project.org/web/packages/dsb/index.html)

R/dsb.r

@@ -64,7 +64,7 @@ DSBNormalizeProtein = function(cell_protein_matrix, empty_drop_matrix, denoise.c
                                use.isotype.control = TRUE, isotype.control.name.vec = NULL,
                                define.pseudocount = FALSE, pseudocount.use,quantile.clipping = FALSE,
                                quantile.clip = c(0.001, 0.9995), return.stats = FALSE){
-  # check names of supplied isotype controls for denoising are in the matrix
+  # error handling
   if(!is.null(isotype.control.name.vec)) {
     if(!all(isotype.control.name.vec %in% rownames(cell_protein_matrix))) {
       stop("the following isotype control cannot be found in the rownames of `cell_protein_matrix`: ",
@@ -74,9 +74,13 @@ DSBNormalizeProtein = function(cell_protein_matrix, empty_drop_matrix, denoise.c
   if (isTRUE(return.stats) & isFALSE(denoise.counts)) {
     stop("set return.stats = FALSE to run dsb if denoise.counts = FALSE")
   }
+  if (isTRUE(use.isotype.control) & is.null(isotype.control.name.vec)) {
+    stop('must specify a vector of isotype control names if use.isotype.control is set to TRUE (recommended)')
+  }
   # convert input data to matrix (e.g. for sparse matrix conversion) and log transform
   adt = cell_protein_matrix %>% as.matrix()
   adtu = empty_drop_matrix %>% as.matrix()
+  # log transform
   if(isTRUE(define.pseudocount)) {
     adtu_log = log(adtu + pseudocount.use)
     adt_log = log(adt + pseudocount.use)

cran-comments.md

@@ -1,6 +1,6 @@
 ## Submission Aug 1 2021 
 
-Submission for version 0.2.0
+Update submission for version 0.2.0
 
 ## Test environments
 * Winbuilder
@@ -17,8 +17,8 @@ Bioconductor does not yet build and check packages for R version 4.2 see https:/
 devtools::check(args = c('--as-cran'))  
 0 errors ✓ | 0 warnings ✓ | 0 notes ✓
 
-**Re. custom license**
-Please refer to Cran team comments from 2021/01/24 
+**Re. custom license used in this package**
+Please refer to Cran team comments from 2021/01/24
 
 "Please only ship the CRAN template for the BSD_3_clause license."  
 Following instructions sent via email 9 Jan, 2021, the CRAN template for BSD-3 (https://cran.r-project.org/web/licenses/BSD_3_clause) is listed "in addition to the alternate BSD text". License documents are referenced in the description as instructed (see email below).