From d828f4d3e769347ac38ed4223f657f574b8dda23 Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Fri, 13 Oct 2017 16:04:18 +1100
Subject: [PATCH] Convert to SingleCellExperiment
---
R/BASiCS-simulate.R | 30 ++++++++++++++++--------------
man/BASiCSSimulate.Rd | 2 +-
2 files changed, 17 insertions(+), 15 deletions(-)
diff --git a/R/BASiCS-simulate.R b/R/BASiCS-simulate.R
index deb56f1..7b80d69 100644
--- a/R/BASiCS-simulate.R
+++ b/R/BASiCS-simulate.R
@@ -14,7 +14,7 @@
#' \code{\link[BASiCS]{BASiCS_Sim}} for more details of how the simulation
#' works.
#'
-#' @return SCESet containing simulated counts
+#' @return SingleCellExperiment containing simulated counts
#'
#' @references
#' Vallejos CA, Marioni JC, Richardson S. BASiCS: Bayesian Analysis of
@@ -45,8 +45,8 @@ BASiCSSimulate <- function(params = newBASiCSParams(), verbose = TRUE, ...) {
nSpikes <- getParam(params, "nSpikes")
nBatches <- getParam(params, "nBatches")
batch.cells <- getParam(params, "batchCells")
-
gene.params <- getParam(params, "gene.params")
+
# Sample gene.params if necessary
if (nrow(gene.params) != nGenes) {
warning("Number of gene.params not equal to nGenes, ",
@@ -102,7 +102,7 @@ BASiCSSimulate <- function(params = newBASiCSParams(), verbose = TRUE, ...) {
counts <- do.call(cbind, counts.list)
- if (verbose) {message("Creating SCESet...")}
+ if (verbose) {message("Creating final dataset...")}
cell.names <- paste0("Cell", seq_len(nCells))
gene.names <- paste0("Gene", seq_len(nGenes))
if (nSpikes > 0) {
@@ -115,22 +115,24 @@ BASiCSSimulate <- function(params = newBASiCSParams(), verbose = TRUE, ...) {
rownames(counts) <- gene.names
colnames(counts) <- cell.names
- phenos <- new("AnnotatedDataFrame",
- data = data.frame(Cell = cell.names,
- Phi = cell.params[, "Phi"],
- S = cell.params[, "S"],
- Batch = batches,
- BatchTheta = thetas[batches]))
- rownames(phenos) <- cell.names
+
+ cells <- data.frame(Cell = cell.names,
+ Phi = cell.params[, "Phi"],
+ S = cell.params[, "S"],
+ Batch = batches,
+ BatchTheta = thetas[batches])
+ rownames(cells) <- cell.names
+
features <- data.frame(Gene = gene.names,
Mean = c(mu, spike.mu),
Delta = c(delta, rep(NA, nSpikes)),
IsSpike = c(rep(FALSE, nGenes), rep(TRUE, nSpikes)))
- features <- new("AnnotatedDataFrame",
- data = features)
rownames(features) <- gene.names
- sim <- newSCESet(countData = counts, phenoData = phenos,
- featureData = features)
+
+ sim <- SingleCellExperiment(assays = list(counts = counts),
+ rowData = features,
+ colData = cells,
+ metadata = list(params = params))
if (verbose) {message("Done!")}
return(sim)
diff --git a/man/BASiCSSimulate.Rd b/man/BASiCSSimulate.Rd
index bf9b325..cc92db0 100644
--- a/man/BASiCSSimulate.Rd
+++ b/man/BASiCSSimulate.Rd
@@ -15,7 +15,7 @@ BASiCSSimulate(params = newBASiCSParams(), verbose = TRUE, ...)
\code{params}.}
}
\value{
-SCESet containing simulated counts
+SingleCellExperiment containing simulated counts
}
\description{
Simulate counts using the BASiCS method.
--
GitLab