Merge branch 'devel'

* devel:
  bump x.y.z versions to odd y after creation of 3_5 branch
  bump x.y.z versions to even y prior to creation of 3_5 branch
  Merge branch 'master' into devel
  Merge branch 'master' into devel
  Merge branch 'master' into devel
  Merge branch 'master' into devel
  Merge branch 'master' into devel
  Merge branch 'master' into devel
  Merge branch 'master' into devel
  Merge branch 'master' into devel
  Merge branch 'master' into devel

R/splat-simulate.R

@@ -550,6 +550,15 @@ splatSimPathCellMeans <- function(sim, params) {
         fData(sim)[[paste0("SigmaFacPath", idx)]] <- sigma.facs
     }
 
+    # Generate non-linear path factors
+    for (idx in seq_along(path.from)) {
+        # Select genes to follow a non-linear path
+        is.nonlinear <- as.logical(rbinom(nGenes, 1, path.nonlinearProb))
+        sigma.facs <- rep(0, nGenes)
+        sigma.facs[is.nonlinear] <- path.sigmaFac
+        fData(sim)[[paste0("SigmaFacPath", idx)]] <- sigma.facs
+    }
+
     # Generate paths. Each path is a matrix with path.length columns and
     # nGenes rows where the expression from each genes changes along the path.
     path.steps <- lapply(seq_along(path.from), function(idx) {

README.md

@@ -80,3 +80,4 @@ doi:10.1101/133173"][preprint].
 [bioc]: https://bioconductor.org/packages/devel/bioc/html/splatter.html
 [vignette]: https://bioconductor.org/packages/devel/bioc/vignettes/splatter/inst/doc/splatter.html
 [preprint]: http://dx.doi.org/10.1101/133173
+

vignettes/splatter.Rmd

@@ -235,7 +235,7 @@ the following steps:
 5. Dropout parameters are estimated by checking if dropout is present and
    fitting a logistic function to the relationship between mean expression and
    proportion of zeros.
-   
+
 For more details of the estimation procedures see `?splatEstimate`.
 
 # Simulating counts