Add port method to splatEstDropout

Fixes Oshlack#133
wenjie2wang · Jan 28, 2022 · 1eec243 · 1eec243
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: splatter
 Type: Package
 Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 1.19.2
-Date: 2022-01-10
+Version: 1.19.3
+Date: 2022-01-28
 Authors@R:
     c(person("Luke", "Zappia", role = c("aut", "cre"),
       email = "luke@lazappi.id.au",

diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,10 @@
 # DEVELOPMENT VERSION
 
+## Version 1.19.3 (2022-01-28)
+
 * Removed duplicated code in splatSimPathCellMeans() (Fixes #131)
+* Add additional fallback method for fitting dropout in splatEstimate()
+  (Fixes #133)
 
 ## Version 1.19.2 (2022-01-10)
 

diff --git a/R/splat-estimate.R b/R/splat-estimate.R
@@ -277,8 +277,16 @@ splatEstDropout <- function(norm.counts, params) {
     error = function(err) {
         warning("Fitting dropout using the Gauss-Newton method failed, ",
                 "using the Golub-Pereyra algorithm instead")
-        nls(y ~ logistic(x, x0 = x0, k = k), data = df,
-            start = list(x0 = 0, k = -1), algorithm = "plinear")
+        tryCatch({
+            nls(y ~ logistic(x, x0 = x0, k = k), data = df,
+                start = list(x0 = 0, k = -1), algorithm = "plinear")
+        },
+        error = function(err) {
+            warning("Fitting dropout using the Golub-Pereyra method failed, ",
+                    "using the nl2sol algorithm instead")
+            nls(y ~ logistic(x, x0 = x0, k = k), data = df,
+                start = list(x0 = 0, k = -1), algorithm = "port")
+        })
     })
 
     #exp.zeros <- dnbinom(0, mu = means, size = 1 / 0.1) * ncol(norm.counts)