From aac2b5d497dda85dcedbd6f557a1148a84032876 Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Mon, 15 Apr 2019 15:51:21 +1000
Subject: [PATCH] Protect against integer overflow in sim functions
Fixes #49
---
R/lun-simulate.R | 8 +++++---
R/simple-simulate.R | 7 ++++---
R/splat-simulate.R | 13 ++++++++-----
3 files changed, 17 insertions(+), 11 deletions(-)
diff --git a/R/lun-simulate.R b/R/lun-simulate.R
index b94c656..526733e 100644
--- a/R/lun-simulate.R
+++ b/R/lun-simulate.R
@@ -105,9 +105,11 @@ lunSimulate <- function(params = newLunParams(), verbose = TRUE, ...) {
rownames(cell.means) <- gene.names
if (verbose) {message("Simulating counts...")}
- counts <- matrix(rnbinom(nGenes * nCells, mu = cell.means,
- size = 1 / count.disp),
- nrow = nGenes, ncol = nCells)
+ counts <- matrix(rnbinom(
+ as.numeric(nGenes) * as.numeric(nCells),
+ mu = cell.means, size = 1 / count.disp
+ ),
+ nrow = nGenes, ncol = nCells)
if (verbose) {message("Creating final dataset...")}
rownames(counts) <- gene.names
diff --git a/R/simple-simulate.R b/R/simple-simulate.R
index 3c074ce..6ca63d3 100644
--- a/R/simple-simulate.R
+++ b/R/simple-simulate.R
@@ -43,9 +43,10 @@ simpleSimulate <- function(params = newSimpleParams(), verbose = TRUE, ...) {
means <- rgamma(nGenes, shape = mean.shape, rate = mean.rate)
if (verbose) {message("Simulating counts...")}
- counts <- matrix(rnbinom(nGenes * nCells, mu = means,
- size = 1 / count.disp),
- nrow = nGenes, ncol = nCells)
+ counts <- matrix(rnbinom(
+ as.numeric(nGenes) * as.numeric(nCells),
+ mu = means, size = 1 / count.disp),
+ nrow = nGenes, ncol = nCells)
if (verbose) {message("Creating final dataset...")}
cell.names <- paste0("Cell", seq_len(nCells))
diff --git a/R/splat-simulate.R b/R/splat-simulate.R
index 6c9a0e7..238dedd 100644
--- a/R/splat-simulate.R
+++ b/R/splat-simulate.R
@@ -646,9 +646,10 @@ splatSimBCVMeans <- function(sim, params) {
bcv <- (bcv.common + (1 / sqrt(base.means.cell)))
}
- means.cell <- matrix(rgamma(nGenes * nCells, shape = 1 / (bcv ^ 2),
- scale = base.means.cell * (bcv ^ 2)),
- nrow = nGenes, ncol = nCells)
+ means.cell <- matrix(rgamma(
+ as.numeric(nGenes) * as.numeric(nCells),
+ shape = 1 / (bcv ^ 2), scale = base.means.cell * (bcv ^ 2)),
+ nrow = nGenes, ncol = nCells)
colnames(means.cell) <- cell.names
rownames(means.cell) <- gene.names
@@ -680,8 +681,10 @@ splatSimTrueCounts <- function(sim, params) {
nCells <- getParam(params, "nCells")
cell.means <- assays(sim)$CellMeans
- true.counts <- matrix(rpois(nGenes * nCells, lambda = cell.means),
- nrow = nGenes, ncol = nCells)
+ true.counts <- matrix(rpois(
+ as.numeric(nGenes) * as.numeric(nCells),
+ lambda = cell.means),
+ nrow = nGenes, ncol = nCells)
colnames(true.counts) <- cell.names
rownames(true.counts) <- gene.names
--
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