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Commit ec40690a authored by Luke Zappia's avatar Luke Zappia
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Rename splat sub functions to differentiate

The splat sub function names were in the same format as the simulation names.
Changed to make it obvious they are different.
parent 7a4b16af
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Package: splatter
Type: Package
Title: Simple Simulation of Single-cell RNA Sequencing Data
Version: 0.4.1
Version: 0.4.2
Date: 2016-10-12
Author: Luke Zappia
Authors@R: as.person(c(
......
......@@ -92,6 +92,14 @@
#' \code{underscore_naming}.
#'
#' @return SCESet object containing the simulated counts and intermediate values
#'
#' @seealso
#' \code{\link{addLibSizes}}, \code{\link{addGeneMeans}},
#' \code{\link{addSingleCellMeans}}, \code{\link{addGroupDE}},
#' \code{\link{addGroupCellMeans}}, \code{\link{addPathDE}},
#' \code{\link{addPathCellMeans}}, \code{\link{addBCVMeans}},
#' \code{\link{addTrueCounts}}, \code{\link{addDropout}}
#'
#' @examples
#' # Simulation with default parameters
#' sim <- splat()
......@@ -164,28 +172,28 @@ splat <- function(params = defaultParams(),
}
if (verbose) {message("Simulating library sizes...")}
sim <- simLibSizes(sim, params)
sim <- addLibSizes(sim, params)
if (verbose) {message("Simulating gene means...")}
sim <- simGeneMeans(sim, params)
sim <- addGeneMeans(sim, params)
if (method == "single") {
sim <- simSingleCellMeans(sim, params)
sim <- addSingleCellMeans(sim, params)
} else if (method == "groups") {
if (verbose) {message("Simulating group DE...")}
sim <- simGroupDE(sim, params)
sim <- addGroupDE(sim, params)
if (verbose) {message("Simulating cell means...")}
sim <- simGroupCellMeans(sim, params)
sim <- addGroupCellMeans(sim, params)
} else {
if (verbose) {message("Simulating path endpoints...")}
sim <- simPathDE(sim, params)
sim <- addPathDE(sim, params)
if (verbose) {message("Simulating path steps...")}
sim <- simPathCellMeans(sim, params)
sim <- addPathCellMeans(sim, params)
}
if (verbose) {message("Simulating BCV...")}
sim <- simBCVMeans(sim, params)
sim <- addBCVMeans(sim, params)
if (verbose) {message("Simulating counts..")}
sim <- simTrueCounts(sim, params)
sim <- addTrueCounts(sim, params)
if (verbose) {message("Simulating dropout...")}
sim <- simDropout(sim, params)
sim <- addDropout(sim, params)
if (verbose) {message("Creating final SCESet...")}
# Create new SCESet to make sure values are calculated correctly
......@@ -236,7 +244,7 @@ splatPaths <- function(params = defaultParams(), verbose = TRUE, ...) {
#'
#' @importFrom Biobase pData pData<-
#' @importFrom stats rlnorm
simLibSizes <- function(sim, params) {
addLibSizes <- function(sim, params) {
nCells <- getParams(params, "nCells")
lib.loc <- getParams(params, "lib.loc")
......@@ -261,7 +269,7 @@ simLibSizes <- function(sim, params) {
#'
#' @importFrom Biobase fData fData<-
#' @importFrom stats rgamma median
simGeneMeans <- function(sim, params) {
addGeneMeans <- function(sim, params) {
nGenes <- getParams(params, "nGenes")
mean.shape <- getParams(params, "mean.shape")
......@@ -302,7 +310,7 @@ simGeneMeans <- function(sim, params) {
#' @return SCESet with added differential expression.
#'
#' @importFrom Biobase fData
simGroupDE <- function(sim, params) {
addGroupDE <- function(sim, params) {
nGenes <- getParams(params, "nGenes")
nGroups <- getParams(params, "nGroups")
......@@ -326,7 +334,7 @@ simGroupDE <- function(sim, params) {
#' Simulate path differential expression
#'
#' Simulate differential expression for path. Similar to
#' \code{\link{simGroupDE}} but care has to be taken to make sure paths are
#' \code{\link{addGroupDE}} but care has to be taken to make sure paths are
#' processed in the correct order.
#'
#' @param sim SCESet to add differential expression to.
......@@ -335,7 +343,7 @@ simGroupDE <- function(sim, params) {
#' @return SCESet with added differential expression.
#'
#' @importFrom Biobase fData
simPathDE <- function(sim, params) {
addPathDE <- function(sim, params) {
nGenes <- getParams(params, "nGenes")
de.prob <- getParams(params, "de.prob")
......@@ -373,7 +381,7 @@ simPathDE <- function(sim, params) {
#' @return SCESet with added cell means.
#'
#' @importFrom Biobase fData pData assayData assayData<-
simSingleCellMeans <- function(sim, params) {
addSingleCellMeans <- function(sim, params) {
nCells <- getParams(params, "nCells")
cell.names <- pData(sim)$Cell
......@@ -403,7 +411,7 @@ simSingleCellMeans <- function(sim, params) {
#' @return SCESet with added cell means.
#'
#' @importFrom Biobase fData pData assayData assayData<-
simGroupCellMeans <- function(sim, params) {
addGroupCellMeans <- function(sim, params) {
nGroups <- getParams(params, "nGroups")
cell.names <- pData(sim)$Cell
......@@ -438,7 +446,7 @@ simGroupCellMeans <- function(sim, params) {
#'
#' @importFrom Biobase fData pData assayData
#' @importFrom stats rbinom
simPathCellMeans <- function(sim, params) {
addPathCellMeans <- function(sim, params) {
nGenes <- getParams(params, "nGenes")
nGroups <- getParams(params, "nGroups")
......@@ -523,7 +531,7 @@ simPathCellMeans <- function(sim, params) {
#'
#' @importFrom Biobase fData pData assayData assayData<-
#' @importFrom stats rchisq rgamma
simBCVMeans <- function(sim, params) {
addBCVMeans <- function(sim, params) {
nGenes <- getParams(params, "nGenes")
nCells <- getParams(params, "nCells")
......@@ -564,7 +572,7 @@ simBCVMeans <- function(sim, params) {
#'
#' @importFrom Biobase fData pData assayData
#' @importFrom stats rpois
simTrueCounts <- function(sim, params) {
addTrueCounts <- function(sim, params) {
nGenes <- getParams(params, "nGenes")
nCells <- getParams(params, "nCells")
......@@ -597,7 +605,7 @@ simTrueCounts <- function(sim, params) {
#'
#' @importFrom Biobase fData pData assayData assayData<-
#' @importFrom stats rbinom
simDropout <- function(sim, params) {
addDropout <- function(sim, params) {
dropout.present <- getParams(params, "dropout.present")
true.counts <- assayData(sim)$TrueCounts
......
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/simulate-splat.R
\name{simBCVMeans}
\alias{simBCVMeans}
\name{addBCVMeans}
\alias{addBCVMeans}
\title{Simulate BCV means}
\usage{
simBCVMeans(sim, params)
addBCVMeans(sim, params)
}
\arguments{
\item{sim}{SCESet to add BCV means to.}
......
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/simulate-splat.R
\name{simDropout}
\alias{simDropout}
\name{addDropout}
\alias{addDropout}
\title{Simulate dropout}
\usage{
simDropout(sim, params)
addDropout(sim, params)
}
\arguments{
\item{sim}{SCESet to add dropout to.}
......
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/simulate-splat.R
\name{simGeneMeans}
\alias{simGeneMeans}
\name{addGeneMeans}
\alias{addGeneMeans}
\title{Simulate gene means}
\usage{
simGeneMeans(sim, params)
addGeneMeans(sim, params)
}
\arguments{
\item{sim}{SCESet to add gene means to.}
......
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/simulate-splat.R
\name{simGroupCellMeans}
\alias{simGroupCellMeans}
\name{addGroupCellMeans}
\alias{addGroupCellMeans}
\title{Simulate group cell means}
\usage{
simGroupCellMeans(sim, params)
addGroupCellMeans(sim, params)
}
\arguments{
\item{sim}{SCESet to add cell means to.}
......
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/simulate-splat.R
\name{simGroupDE}
\alias{simGroupDE}
\name{addGroupDE}
\alias{addGroupDE}
\title{Simulate group differential expression}
\usage{
simGroupDE(sim, params)
addGroupDE(sim, params)
}
\arguments{
\item{sim}{SCESet to add differential expression to.}
......
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/simulate-splat.R
\name{simLibSizes}
\alias{simLibSizes}
\name{addLibSizes}
\alias{addLibSizes}
\title{Simulate library sizes}
\usage{
simLibSizes(sim, params)
addLibSizes(sim, params)
}
\arguments{
\item{sim}{SCESet to add library size to.}
......
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/simulate-splat.R
\name{simPathCellMeans}
\alias{simPathCellMeans}
\name{addPathCellMeans}
\alias{addPathCellMeans}
\title{Simulate path cell means}
\usage{
simPathCellMeans(sim, params)
addPathCellMeans(sim, params)
}
\arguments{
\item{sim}{SCESet to add cell means to.}
......
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/simulate-splat.R
\name{simPathDE}
\alias{simPathDE}
\name{addPathDE}
\alias{addPathDE}
\title{Simulate path differential expression}
\usage{
simPathDE(sim, params)
addPathDE(sim, params)
}
\arguments{
\item{sim}{SCESet to add differential expression to.}
......@@ -16,7 +16,7 @@ SCESet with added differential expression.
}
\description{
Simulate differential expression for path. Similar to
\code{\link{simGroupDE}} but care has to be taken to make sure paths are
\code{\link{addGroupDE}} but care has to be taken to make sure paths are
processed in the correct order.
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/simulate-splat.R
\name{simSingleCellMeans}
\alias{simSingleCellMeans}
\name{addSingleCellMeans}
\alias{addSingleCellMeans}
\title{Simulate single population cell means}
\usage{
simSingleCellMeans(sim, params)
addSingleCellMeans(sim, params)
}
\arguments{
\item{sim}{SCESet to add cell means to.}
......
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/simulate-splat.R
\name{simTrueCounts}
\alias{simTrueCounts}
\name{addTrueCounts}
\alias{addTrueCounts}
\title{Simulate true counts}
\usage{
simTrueCounts(sim, params)
addTrueCounts(sim, params)
}
\arguments{
\item{sim}{SCESet to add true counts to.}
......
......@@ -117,4 +117,11 @@ sim <- splat(params, mean.rate = 0.6, out.prob = 0.2)
# Simulate paths instead of groups
sim <- splat(method = "paths")
}
\seealso{
\code{\link{addLibSizes}}, \code{\link{addGeneMeans}},
\code{\link{addSingleCellMeans}}, \code{\link{addGroupDE}},
\code{\link{addGroupCellMeans}}, \code{\link{addPathDE}},
\code{\link{addPathCellMeans}}, \code{\link{addBCVMeans}},
\code{\link{addTrueCounts}}, \code{\link{addDropout}}
}
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