Accommodate changes from DropletUtils::emptyDrops()

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: OSCA.advanced
 Title: Advanced Single-Cell Analysis
-Version: 1.15.2
-Date: 2024-07-01
+Version: 1.15.3
+Date: 2025-03-31
 Authors@R: c( 
         person('Robert', 'Amezquita', role = 'aut'), 
         person('Aaron', 'Lun', role = 'aut'), 

inst/book/cell-cycle.Rmd

@@ -151,7 +151,7 @@ tab
 singler.assignments <- assignments
 stopifnot(tab["G1",1] > 0.5 * sum(tab[,1]))
 stopifnot(tab["G2M",2] > 0.5 * sum(tab[,2]))
-stopifnot(tab["G1",3] > 0.5 * sum(tab[,3]))
+stopifnot(tab["G1",3] > 0.45 * sum(tab[,3]))
 stopifnot(tab["G2M",4] > 0.5 * sum(tab[,4]))
 ```
 

inst/book/doublet-detection.Rmd

@@ -255,7 +255,12 @@ The barcode-rank plots are quite similar to what one might expect from gene expr
 library(DropletUtils)
 
 set.seed(101)
-hash.calls <- emptyDrops(counts(hto.sce), by.rank=40000)
+# HTO counts tend to exhibit stronger overdispersion (i.e., lower `alpha` in 
+# the `emptyDrops()` calculations), increasing the risk of violating 
+# `emptyDrops()`'s distributional assumptions.
+# Setting `alpha=NULL` estimates alpha using maximum likelihood; see 
+# `?emptyDrops` for details.
+hash.calls <- emptyDrops(counts(hto.sce), by.rank=40000, alpha=NULL)
 is.cell <- which(hash.calls$FDR <= 0.001)
 length(is.cell)
 

inst/book/droplet-processing.Rmd

@@ -303,7 +303,6 @@ hist(log10(e.out.hto$Total[is.cell.hto]), xlab="Log[10] HTO count", main="")
 
 While both approaches are valid, we tend to favor the cell calls derived from the gene matrix as this directly indicates that a cell is present in the droplet.
 Indeed, at least a few libraries have very high total HTO counts yet very low total gene counts (Figure \@ref(fig:hto-total-comp)), suggesting that the presence of HTOs may not always equate to successful capture of that cell's transcriptome.
-HTO counts also tend to exhibit stronger overdispersion (i.e., lower `alpha` in the `emptyDrops()` calculations), increasing the risk of violating `emptyDrops()`'s distributional assumptions.
 
 ```{r hto-total-comp, fig.cap="Total HTO counts plotted against the total gene counts for each library in the cell line mixture dataset. Each point represents a library while the dotted lines represent the thresholds below which libraries were assumed to be empty droplets."}
 table(HTO=is.cell.hto, Genes=is.cell, useNA="always")
@@ -316,7 +315,6 @@ abline(h=metadata(e.out.hto)$lower, col="blue", lwd=2, lty=2)
 
 ```{r, echo=FALSE}
 # Sanity checks for trash-talk above.
-stopifnot(metadata(e.out.hto)$alpha < 50 * metadata(e.out.gene)$alpha)
 stopifnot(sum(e.out.gene$Total < 100 & e.out.hto$Total > 1000) > 50)
 ```