diff --git a/R/scDD-estimate.R b/R/scDD-estimate.R index d75083d6e6b5645a8abde103d7bdb79dc66c9c68..3461444456c628f2480ba5c28f412a431a5ed481 100644 --- a/R/scDD-estimate.R +++ b/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) diff --git a/man/SplatParams.Rd b/man/SplatParams.Rd index f023311b27a5a0f9b3e47328c4d2a923e2949772..10d5b48138a947fe19404d21950ededea23654a2 100644 --- a/man/SplatParams.Rd +++ b/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 diff --git a/man/setParams.Rd b/man/setParams.Rd index 05e8955b3a6195bc611e47fb18cf1339683db283..a3843db3419a28fcf626184c8a47131e608a8b9d 100644 --- a/man/setParams.Rd +++ b/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}.} } diff --git a/man/setParamsUnchecked.Rd b/man/setParamsUnchecked.Rd index 43d6ee8e316c071837e0397e77ffce098888d28a..a99d38f8a1b007a1c34d075084374289c362512d 100644 --- a/man/setParamsUnchecked.Rd +++ b/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}.} }