Document lun2Simulate and add tests

DESCRIPTION

 Package: splatter
 Type: Package
 Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 0.7.4
+Version: 0.7.5
 Date: 2016-10-15
 Author: Luke Zappia
 Authors@R: as.person(c(

R/lun-simulate.R

@@ -24,7 +24,7 @@
 #'
 #' @references
 #' Lun ATL, Bach K, Marioni JC. Pooling across cells to normalize single-cell
-#' RNA sequencing data with many zero counts. Genome Biology (2016)
+#' RNA sequencing data with many zero counts. Genome Biology (2016).
 #'
 #' Paper: \url{dx.doi.org/10.1186/s13059-016-0947-7}
 #'

R/lun2-simulate.R

@@ -11,8 +11,24 @@
 #'        \code{params}.
 #'
 #' @details
+#' The Lun2 simulation uses a negative-binomial distribution where the means and
+#' dispersions have been sampled from a real dataset
+#' (using \code{\link{lun2Estimate}}). The other core feature of the Lun2
+#' simulation is the addition of plate effects. Differential expression can be
+#' added between two groups of plates (an "ingroup" and all other plates).
+#' Library size factors are also applied and optionally a zero-inflated
+#' negative-binomial can be used.
 #'
 #' @return SCESet containing simulated counts.
+#'
+#' @references
+#' Lun ATL, Marioni JC. Overcoming confounding plate effects in differential
+#' expression analyses of single-cell RNA-seq data. bioRxiv (2016).
+#'
+#' Paper: \url{dx.doi.org/10.1101/073973}
+#'
+#' Code: \url{https://github.com/MarioniLab/PlateEffects2016}
+#'
 #' @examples
 #' sim <- lun2Simulate()
 #' @export

man/lun2Simulate.Rd

@@ -25,9 +25,23 @@ and Marioni "Overcoming confounding plate effects in differential expression
 analyses of single-cell RNA-seq data".
 }
 \details{
-
+The Lun2 simulation uses a negative-binomial distribution where the means and
+dispersions have been sampled from a real dataset
+(using \code{\link{lun2Estimate}}). The other core feature of the Lun2
+simulation is the addition of plate effects. Differential expression can be
+added between two groups of plates (an "ingroup" and all other plates).
+Library size factors are also applied and optionally a zero-inflated
+negative-binomial can be used.
 }
 \examples{
 sim <- lun2Simulate()
 }
+\references{
+Lun ATL, Marioni JC. Overcoming confounding plate effects in differential
+expression analyses of single-cell RNA-seq data. bioRxiv (2016).
+
+Paper: \url{dx.doi.org/10.1101/073973}
+
+Code: \url{https://github.com/MarioniLab/PlateEffects2016}
+}
 

man/lunSimulate.Rd

@@ -39,7 +39,7 @@ sim <- lunSimulate()
 }
 \references{
 Lun ATL, Bach K, Marioni JC. Pooling across cells to normalize single-cell
-RNA sequencing data with many zero counts. Genome Biology (2016)
+RNA sequencing data with many zero counts. Genome Biology (2016).
 
 Paper: \url{dx.doi.org/10.1186/s13059-016-0947-7}
 

tests/testthat/test-lun2-simulate.R

+context("Lun2 simulation")
+
+test_that("Lun2 simulation output is valid", {
+    expect_true(validObject(lun2Simulate()))
+    expect_true(validObject(lun2Simulate(de.nGenes = 100)))
+    expect_true(validObject(lun2Simulate(zinb = TRUE)))
+})
\ No newline at end of file