From 9267f271954deb646ad972a2e098c6de43d3354e Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Thu, 5 Oct 2017 12:29:53 +1100
Subject: [PATCH] Convert mfaSimulate output to counts
---
R/mfa-simulate.R | 15 ++++++++++-----
man/mfaSimulate.Rd | 7 ++++---
2 files changed, 14 insertions(+), 8 deletions(-)
diff --git a/R/mfa-simulate.R b/R/mfa-simulate.R
index 70d171d..bca30e7 100644
--- a/R/mfa-simulate.R
+++ b/R/mfa-simulate.R
@@ -10,9 +10,10 @@
#' @details
#' This function is just a wrapper around \code{\link[mfa]{create_synthetic}}
#' that takes a \code{\link{MFAParams}}, runs the simulation then converts the
-#' output to a \code{\link[SingleCellExperiment]{SingleCellExperiment}} object.
-#' See \code{\link[mfa]{create_synthetic}} and the mfa paper for more details
-#' about how the simulation works.
+#' output from log-expression to counts and returns a
+#' \code{\link[SingleCellExperiment]{SingleCellExperiment}} object. See
+#' \code{\link[mfa]{create_synthetic}} and the mfa paper for more details about
+#' how the simulation works.
#'
#' @return SingleCellExperiment containing simulated counts
#'
@@ -57,7 +58,10 @@ mfaSimulate <- function(params = newMFAParams(), verbose = TRUE, ...) {
cell.names <- paste0("Cell", seq_len(nCells))
gene.names <- paste0("Gene", seq_len(nGenes))
- counts <- t(mfa.sim$X)
+ exprs <- t(mfa.sim$X)
+ counts <- 2 ^ exprs - 1
+ counts[counts < 0] <- 0
+ counts <- round(counts)
rownames(counts) <- gene.names
colnames(counts) <- cell.names
@@ -75,7 +79,8 @@ mfaSimulate <- function(params = newMFAParams(), verbose = TRUE, ...) {
DeltaBranch2 = mfa.sim$delta[, 2])
rownames(features) <- gene.names
- sim <- SingleCellExperiment(assays = list(counts = counts),
+ sim <- SingleCellExperiment(assays = list(counts = counts,
+ LogExprs = exprs),
rowData = features,
colData = cells,
metadata = list(params = params))
diff --git a/man/mfaSimulate.Rd b/man/mfaSimulate.Rd
index 7f7e356..ec2a98e 100644
--- a/man/mfaSimulate.Rd
+++ b/man/mfaSimulate.Rd
@@ -23,9 +23,10 @@ Simulate a bifurcating pseudotime path using the mfa method.
\details{
This function is just a wrapper around \code{\link[mfa]{create_synthetic}}
that takes a \code{\link{MFAParams}}, runs the simulation then converts the
-output to a \code{\link[SingleCellExperiment]{SingleCellExperiment}} object.
-See \code{\link[mfa]{create_synthetic}} and the mfa paper for more details
-about how the simulation works.
+output from log-expression to counts and returns a
+\code{\link[SingleCellExperiment]{SingleCellExperiment}} object. See
+\code{\link[mfa]{create_synthetic}} and the mfa paper for more details about
+how the simulation works.
}
\examples{
sim <- mfaSimulate()
--
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