Document Lun2Params

DESCRIPTION

 Package: splatter
 Type: Package
 Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 0.7.1
+Version: 0.7.2
 Date: 2016-10-14
 Author: Luke Zappia
 Authors@R: as.person(c(

R/AllClasses.R

@@ -293,6 +293,39 @@ setClass("LunParams",
 #'   \item{\code{nGenes}}{The number of genes to simulate.}
 #'   \item{\code{nCells}}{The number of cells to simulate.}
 #'   \item{\code{[seed]}}{Seed to use for generating random numbers.}
+#'   \item{\code{[nPlates]}}{The number of plates to simulate.}
+#'   \item{\emph{Plate parameters}}{
+#'     \describe{
+#'       \item{\code{path.ingroup}}{Plates considered to be part of the
+#'       "ingroup".}
+#'       \item{\code{path.mod}}{Plate effect modifier factor. The plate effect
+#'       variance is divided by this value.}
+#'       \item{\code{plate.var}}{Plate effect variance.}
+#'     }
+#'   }
+#'   \item{\emph{Gene parameters}}{
+#'     \describe{
+#'       \item{\code{gene.means}}{Mean expression for each gene.}
+#'       \item{\code{gene.disps}}{Dispersion for each gene.}
+#'       \item{\code{gene.ziMeans}}{Zero-inflated gene means.}
+#'       \item{\code{gene.ziDisps}}{Zero-inflated gene dispersions.}
+#'       \item{\code{gene.ziProps}}{Zero-inflated gene zero proportions.}
+#'     }
+#'   }
+#'   \item{\emph{Cell parameters}}{
+#'     \describe{
+#'       \item{\code{cell.plates}}{Plate that each cell comes from.}
+#'       \item{\code{cell.libSizes}}{Library size for each cell.}
+#'       \item{\code{cell.libMod}}{Modifier factor for library sizes.
+#'       The library sizes are multiplied by this value.}
+#'     }
+#'   }
+#'   \item{\emph{Differential expression parameters}}{
+#'     \describe{
+#'       \item{\code{de.nGenes}}{Number of differentially expressed genes.}
+#'       \item{\code{de.fc}}{Fold change for differentially expressed genes.}
+#'     }
+#'   }
 #' }
 #'
 #' The parameters not shown in brackets can be estimated from real data using
@@ -318,8 +351,7 @@ setClass("Lun2Params",
                    cell.libSizes = "numeric",
                    cell.libMod = "numeric",
                    de.nGenes = "numeric",
-                   de.fc = "numeric",
-                   useZINB = "logical"),
+                   de.fc = "numeric"),
          prototype = prototype(nPlates = 1,
                                cell.plates = rep(1, 100),
                                plate.ingroup = 1,
@@ -333,5 +365,4 @@ setClass("Lun2Params",
                                cell.libSizes = rep(70000, 100),
                                cell.libMod = 1,
                                de.nGenes = 0,
-                               de.fc = 3,
-                               useZINB = FALSE))
\ No newline at end of file
+                               de.fc = 3))
\ No newline at end of file

R/Lun2Params-methods.R

@@ -42,8 +42,7 @@ setValidity("Lun2Params", function(object) {
                                                 len = nCells),
                 cell.libMod = checkNumber(v$cell.libMod, lower = 0),
                 de.nGene = checkInt(v$de.nGenes, lower = 0),
-                de.fc = checkNumber(v$de.fc, lower = 0),
-                useZINB = checkLogical(v$useZINB, len = 1))
+                de.fc = checkNumber(v$de.fc, lower = 0))
 
     if (all(checks == TRUE)) {
         valid <- TRUE

man/Lun2Params.Rd

@@ -17,6 +17,39 @@ The Lun2 simulation uses the following parameters:
   \item{\code{nGenes}}{The number of genes to simulate.}
   \item{\code{nCells}}{The number of cells to simulate.}
   \item{\code{[seed]}}{Seed to use for generating random numbers.}
+  \item{\code{[nPlates]}}{The number of plates to simulate.}
+  \item{\emph{Plate parameters}}{
+    \describe{
+      \item{\code{path.ingroup}}{Plates considered to be part of the
+      "ingroup".}
+      \item{\code{path.mod}}{Plate effect modifier factor. The plate effect
+      variance is divided by this value.}
+      \item{\code{plate.var}}{Plate effect variance.}
+    }
+  }
+  \item{\emph{Gene parameters}}{
+    \describe{
+      \item{\code{gene.means}}{Mean expression for each gene.}
+      \item{\code{gene.disps}}{Dispersion for each gene.}
+      \item{\code{gene.ziMeans}}{Zero-inflated gene means.}
+      \item{\code{gene.ziDisps}}{Zero-inflated gene dispersions.}
+      \item{\code{gene.ziProps}}{Zero-inflated gene zero proportions.}
+    }
+  }
+  \item{\emph{Cell parameters}}{
+    \describe{
+      \item{\code{cell.plates}}{Plate that each cell comes from.}
+      \item{\code{cell.libSizes}}{Library size for each cell.}
+      \item{\code{cell.libMod}}{Modifier factor for library sizes.
+      The library sizes are multiplied by this value.}
+    }
+  }
+  \item{\emph{Differential expression parameters}}{
+    \describe{
+      \item{\code{de.nGenes}}{Number of differentially expressed genes.}
+      \item{\code{de.fc}}{Fold change for differentially expressed genes.}
+    }
+  }
 }
 
 The parameters not shown in brackets can be estimated from real data using