Run checks

R/scDD-estimate.R

@@ -36,6 +36,11 @@ scDDEstimate.SCESet <- function(counts, conditions, params = newSCDDParams()) {
 #' @export
 scDDEstimate.matrix <- function(counts, conditions, params = newSCDDParams()) {
 
+    if (!requireNamespace("scDD", quietly = TRUE)) {
+        stop("The scDD simulation requires the 'scDD' package. ",
+             "See https://github.com/kdkorthauer/scDD for installation.")
+    }
+
     checkmate::assertClass(params, "SCDDParams")
     checkmate::assertIntegerish(conditions, len = ncol(counts), lower = 1,
                                 upper = 2)

man/SplatParams.Rd

@@ -52,7 +52,7 @@ The Splatter simulation requires the following parameters:
     \describe{
       \item{\code{[de.prob]}}{Probability that a gene is differentially
       expressed in a group. Can be a vector.}
-      \item{\code{[de.loProb]}}{Probability that differentially expressed
+      \item{\code{[de.loProb]}}{Probability that a differentially expressed
       gene is down-regulated. Can be a vector.}
       \item{\code{[de.facLoc]}}{Location (meanlog) parameter for the
       differential expression factor log-normal distribution. Can be a

man/setParams.Rd

@@ -4,7 +4,7 @@
 \alias{setParams}
 \title{Set parameters}
 \usage{
-setParams(params, update = NULL, checkValid = TRUE, ...)
+setParams(params, update = NULL, ...)
 }
 \arguments{
 \item{params}{Params object to set parameters in.}
@@ -12,8 +12,6 @@ setParams(params, update = NULL, checkValid = TRUE, ...)
 \item{update}{list of parameters to set where \code{names(update)} are the
 names of the parameters to set and the items in the list are values.}
 
-\item{checkValid}{logical. Whether to check set object is valid.}
-
 \item{...}{additional parameters to set. These are combined with any
 parameters specified in \code{update}.}
 }

man/setParamsUnchecked.Rd

@@ -4,7 +4,7 @@
 \alias{setParamsUnchecked}
 \title{Set parameters UNCHECKED}
 \usage{
-setParamsUnchecked(params, update = NULL, checkValid = TRUE, ...)
+setParamsUnchecked(params, update = NULL, ...)
 }
 \arguments{
 \item{params}{Params object to set parameters in.}
@@ -12,8 +12,6 @@ setParamsUnchecked(params, update = NULL, checkValid = TRUE, ...)
 \item{update}{list of parameters to set where \code{names(update)} are the
 names of the parameters to set and the items in the list are values.}
 
-\item{checkValid}{logical. Whether to check set object is valid.}
-
 \item{...}{additional parameters to set. These are combined with any
 parameters specified in \code{update}.}
 }