From e28ab57433cfda34c40d4776a776d1ad353b7ead Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Thu, 13 Oct 2016 19:38:31 +1100
Subject: [PATCH] Run checks
---
DESCRIPTION | 5 +++--
NAMESPACE | 1 +
R/params-functions.R | 4 ++--
R/simple-estimate.R | 10 +++++-----
R/simple-simulate.R | 1 +
{tests/testthat => TMP}/test-params.R | 0
{tests/testthat => TMP}/test-simulate-lun.R | 0
{tests/testthat => TMP}/test-simulate-splat.R | 0
man/estimateSimpleParams.Rd | 12 +++++++++---
man/getParams.Rd | 2 +-
man/setParams.Rd | 2 +-
man/simpleEstimate.Rd | 11 -----------
tests/testthat/test-simulate-simple.R | 2 +-
13 files changed, 24 insertions(+), 26 deletions(-)
rename {tests/testthat => TMP}/test-params.R (100%)
rename {tests/testthat => TMP}/test-simulate-lun.R (100%)
rename {tests/testthat => TMP}/test-simulate-splat.R (100%)
delete mode 100644 man/simpleEstimate.Rd
diff --git a/DESCRIPTION b/DESCRIPTION
index 7add111..812c8ab 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: splatter
Type: Package
Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 0.6.3
+Version: 0.6.4
Date: 2016-10-13
Author: Luke Zappia
Authors@R: as.person(c(
@@ -25,7 +25,8 @@ Imports:
locfit,
akima,
Biobase,
- checkmate
+ checkmate,
+ methods
Suggests:
testthat
biocViews: SingleCell, RNASeq, Transcriptomics, GeneExpression, Sequencing,
diff --git a/NAMESPACE b/NAMESPACE
index 497ca4f..40e112a 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -10,6 +10,7 @@ export(setParam)
export(setParams)
export(simpleSimulate)
exportClasses(SimpleParams)
+importFrom(scater,newSCESet)
importFrom(stats,median)
importFrom(stats,rgamma)
importFrom(stats,rnbinom)
diff --git a/R/params-functions.R b/R/params-functions.R
index a7d07d1..c795020 100644
--- a/R/params-functions.R
+++ b/R/params-functions.R
@@ -7,7 +7,7 @@
#'
#' @return List with the values of the selected parameters.
#' @examples
-#' params <- simpleParams()
+#' params <- newSimpleParams()
#' getParams(params, c("nGenes", "nCells", "mean.rate"))
#' @export
getParams <- function(params, names) {
@@ -37,7 +37,7 @@ getParams <- function(params, names) {
#'
#' @return Params object with updated values.
#' @examples
-#' params <- simpleParams()
+#' params <- newSimpleParams()
#' params
#' # Set individually
#' params <- setParams(params, nGenes = 1000, nCells = 50)
diff --git a/R/simple-estimate.R b/R/simple-estimate.R
index 60194bc..6474f19 100644
--- a/R/simple-estimate.R
+++ b/R/simple-estimate.R
@@ -2,8 +2,8 @@
#'
#' Estimate simulation parameters for the simple simulation from a real dataset.
#'
-#' @param x either a counts matrix or an SCESet object containing count data to
-#' estimate parameters from.
+#' @param data either a counts matrix or an SCESet object containing count data
+#' to estimate parameters from.
#' @param params SimpleParams object to store estimated values in.
#'
#' @details
@@ -24,14 +24,14 @@ estimateSimpleParams <- function(data, params = newSimpleParams()) {
UseMethod("estimateSimpleParams")
}
-#' @rdname simpleEstimate
+#' @rdname estimateSimpleParams
#' @export
estimateSimpleParams.SCESet <- function(data, params = newSimpleParams()) {
- counts <- scater::counts(x)
+ counts <- scater::counts(data)
estimateSimpleParams(counts, params)
}
-#' @rdname simpleEstimate
+#' @rdname estimateSimpleParams
#' @importFrom stats median
#' @export
estimateSimpleParams.matrix <- function(data, params = newSimpleParams()) {
diff --git a/R/simple-simulate.R b/R/simple-simulate.R
index 7d9b250..86cc762 100644
--- a/R/simple-simulate.R
+++ b/R/simple-simulate.R
@@ -22,6 +22,7 @@
#' sim <- simpleSimulate(nGenes = 1000, nCells = 50)
#' @export
#' @importFrom stats rgamma rnbinom
+#' @importFrom scater newSCESet
simpleSimulate <- function(params = newSimpleParams(), verbose = TRUE, ...) {
checkmate::assertClass(params, "SimpleParams")
diff --git a/tests/testthat/test-params.R b/TMP/test-params.R
similarity index 100%
rename from tests/testthat/test-params.R
rename to TMP/test-params.R
diff --git a/tests/testthat/test-simulate-lun.R b/TMP/test-simulate-lun.R
similarity index 100%
rename from tests/testthat/test-simulate-lun.R
rename to TMP/test-simulate-lun.R
diff --git a/tests/testthat/test-simulate-splat.R b/TMP/test-simulate-splat.R
similarity index 100%
rename from tests/testthat/test-simulate-splat.R
rename to TMP/test-simulate-splat.R
diff --git a/man/estimateSimpleParams.Rd b/man/estimateSimpleParams.Rd
index 8623b2e..b20c902 100644
--- a/man/estimateSimpleParams.Rd
+++ b/man/estimateSimpleParams.Rd
@@ -2,15 +2,21 @@
% Please edit documentation in R/simple-estimate.R
\name{estimateSimpleParams}
\alias{estimateSimpleParams}
+\alias{estimateSimpleParams.SCESet}
+\alias{estimateSimpleParams.matrix}
\title{Estimate simple simulation parameters}
\usage{
estimateSimpleParams(data, params = newSimpleParams())
+
+\method{estimateSimpleParams}{SCESet}(data, params = newSimpleParams())
+
+\method{estimateSimpleParams}{matrix}(data, params = newSimpleParams())
}
\arguments{
-\item{params}{SimpleParams object to store estimated values in.}
+\item{data}{either a counts matrix or an SCESet object containing count data
+to estimate parameters from.}
-\item{x}{either a counts matrix or an SCESet object containing count data to
-estimate parameters from.}
+\item{params}{SimpleParams object to store estimated values in.}
}
\value{
SimpleParams object containing the estimated parameters.
diff --git a/man/getParams.Rd b/man/getParams.Rd
index b891230..e9a81af 100644
--- a/man/getParams.Rd
+++ b/man/getParams.Rd
@@ -18,7 +18,7 @@ List with the values of the selected parameters.
Get multiple parameter values from a Params object.
}
\examples{
-params <- simpleParams()
+params <- newSimpleParams()
getParams(params, c("nGenes", "nCells", "mean.rate"))
}
diff --git a/man/setParams.Rd b/man/setParams.Rd
index a49e57b..a3843db 100644
--- a/man/setParams.Rd
+++ b/man/setParams.Rd
@@ -29,7 +29,7 @@ collecting parameter values in some way) or individually (useful when setting
them manually), see examples.
}
\examples{
-params <- simpleParams()
+params <- newSimpleParams()
params
# Set individually
params <- setParams(params, nGenes = 1000, nCells = 50)
diff --git a/man/simpleEstimate.Rd b/man/simpleEstimate.Rd
deleted file mode 100644
index d58acfd..0000000
--- a/man/simpleEstimate.Rd
+++ /dev/null
@@ -1,11 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simple-estimate.R
-\name{estimateSimpleParams.SCESet}
-\alias{estimateSimpleParams.SCESet}
-\alias{estimateSimpleParams.matrix}
-\usage{
-\method{estimateSimpleParams}{SCESet}(data, params = newSimpleParams())
-
-\method{estimateSimpleParams}{matrix}(data, params = newSimpleParams())
-}
-
diff --git a/tests/testthat/test-simulate-simple.R b/tests/testthat/test-simulate-simple.R
index 832c34d..81d98d0 100644
--- a/tests/testthat/test-simulate-simple.R
+++ b/tests/testthat/test-simulate-simple.R
@@ -1,5 +1,5 @@
context("simple simulation")
test_that("simple simulation output is valid", {
- expect_true(validObject(simSimple()))
+ expect_true(validObject(simpleSimulate()))
})
--
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