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removes sparse to dense matrix conversion #8

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removes sparse to dense matrix conversion #8

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2 changes: 1 addition & 1 deletion R/classifySex.R
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Expand Up @@ -65,7 +65,7 @@ classifySex<-function(x, genome=NULL, qc = TRUE)
{
# Perform some checks on the data
if(is.null(x)) stop("Counts matrix missing")
x <- as.matrix(x)
# x <- as.matrix(x)
if(is.null(genome)){
message("Genome not specified. Human genome used. Options are 'Hs' for
human and 'Mm' for mouse. We currently don't support other genomes.")
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2 changes: 1 addition & 1 deletion R/findMFDoublet.R
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Expand Up @@ -50,7 +50,7 @@ findMfDoublet<-function(x, genome=NULL, qc = FALSE)
{
# Perform some checks on the data
if (is.null(x)) stop("Counts matrix missing")
x <- as.matrix(x)
# x <- as.matrix(x)

if (is.null(genome)){
message("Genome not specified. Human genome used. Options are 'Hs' for
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2 changes: 1 addition & 1 deletion R/lognormCounts.R
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Expand Up @@ -19,7 +19,7 @@ lognormCounts <- function(x, log = TRUE, prior.count = 0.5, lib.size)
# Belinda Phipson
# 26 February 2020
{
x <- as.matrix(x)
# x <- as.matrix(x)
#lib.size <- colSums(x)
M <- median(lib.size)
if(log){
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2 changes: 1 addition & 1 deletion R/preprocess.R
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Expand Up @@ -72,7 +72,7 @@
#'
preprocess<- function(x, genome=genome, qc=qc){

x <- as.matrix(x)
# x <- as.matrix(x)
row.names(x)<- toupper(row.names(x))

if (is.null(row.names(x))){
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2 changes: 1 addition & 1 deletion R/preprocessDb.R
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Expand Up @@ -39,7 +39,7 @@

preprocessDb<- function(x, genome=genome, qc=qc){

x <- as.matrix(x)
# x <- as.matrix(x)
row.names(x)<- toupper(row.names(x))

if (length(unique(colnames(x))) != ncol(x)){
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