From a681f8648161f158b043b0a25a602651c23d0b1a Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Thu, 5 Oct 2017 12:15:50 +1100
Subject: [PATCH] Convert phenoSimulate output to counts
---
R/pheno-simulate.R | 12 +++++++++---
man/phenoSimulate.Rd | 4 +++-
2 files changed, 12 insertions(+), 4 deletions(-)
diff --git a/R/pheno-simulate.R b/R/pheno-simulate.R
index 70042e4..ff0e4c1 100644
--- a/R/pheno-simulate.R
+++ b/R/pheno-simulate.R
@@ -11,7 +11,9 @@
#' This function is just a wrapper around
#' \code{\link[phenopath]{simulate_phenopath}} that takes a
#' \code{\link{PhenoParams}}, runs the simulation then converts the
-#' output to a \code{\link[SingleCellExperiment]{SingleCellExperiment}} object.
+#' output from log-counts to counts and returns a
+#' \code{\link[SingleCellExperiment]{SingleCellExperiment}} object. The original
+#' simulated log-expression values are returned in the \code{LogExprs} asssay.
#' See \code{\link[phenopath]{simulate_phenopath}} and the PhenoPath paper for
#' more details about how the simulation works.
#'
@@ -59,7 +61,10 @@ phenoSimulate <- function(params = newPhenoParams(), verbose = TRUE, ...) {
cell.names <- paste0("Cell", seq_len(nCells))
gene.names <- paste0("Gene", seq_len(nGenes))
- counts <- t(pheno.sim$y)
+ exprs <- t(pheno.sim$y)
+ counts <- 2 ^ exprs - 1
+ counts[counts < 0] <- 0
+ counts <- round(counts)
rownames(counts) <- gene.names
colnames(counts) <- cell.names
@@ -75,7 +80,8 @@ phenoSimulate <- function(params = newPhenoParams(), verbose = TRUE, ...) {
Regime = pheno.sim$parameters$regime)
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/phenoSimulate.Rd b/man/phenoSimulate.Rd
index 2effe20..ff60d00 100644
--- a/man/phenoSimulate.Rd
+++ b/man/phenoSimulate.Rd
@@ -24,7 +24,9 @@ Simulate counts from a pseudotime trajectory using the PhenoPath method.
This function is just a wrapper around
\code{\link[phenopath]{simulate_phenopath}} that takes a
\code{\link{PhenoParams}}, runs the simulation then converts the
-output to a \code{\link[SingleCellExperiment]{SingleCellExperiment}} object.
+output from log-counts to counts and returns a
+\code{\link[SingleCellExperiment]{SingleCellExperiment}} object. The original
+simulated log-expression values are returned in the \code{LogExprs} asssay.
See \code{\link[phenopath]{simulate_phenopath}} and the PhenoPath paper for
more details about how the simulation works.
}
--
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