From ceefcda701b6a833a1e49e1169184d23aabdf4fd Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Sun, 16 Oct 2016 16:23:12 +1100
Subject: [PATCH] Run checks
---
R/scDD-estimate.R | 5 +++++
man/SplatParams.Rd | 2 +-
man/setParams.Rd | 4 +---
man/setParamsUnchecked.Rd | 4 +---
4 files changed, 8 insertions(+), 7 deletions(-)
diff --git a/R/scDD-estimate.R b/R/scDD-estimate.R
index d75083d..3461444 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 f023311..10d5b48 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 05e8955..a3843db 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 43d6ee8..a99d38f 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}.}
}
--
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