From 5f51977e42329946eab10d9806482664f1c0c303 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jens=20Preu=C3=9Fner?= <Jens.Preussner@mpi-bn.mpg.de>
Date: Tue, 2 Oct 2018 13:45:31 +0200
Subject: [PATCH] Speed up rds creation

---
 src/createSCE_kallisto.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/createSCE_kallisto.R b/src/createSCE_kallisto.R
index 5f525b7..bf13298 100644
--- a/src/createSCE_kallisto.R
+++ b/src/createSCE_kallisto.R
@@ -41,7 +41,7 @@ expression <- list(umi = umi_counts)
 #
 if (snakemake@config$container$annotate) {
   ec_members %>%
-    lapply(function(m) {unique(tx2gene[m, "gene"])}) -> ec2gene
+    lapply(function(m) {unique(as.character(tx2gene[m, "gene"]))}) -> ec2gene
 
   bm <- biomaRt::getBM(c(snakemake@config$container$biomart$filter, 'external_gene_name'),
                        filters = snakemake@config$container$biomart$filter,
@@ -51,7 +51,7 @@ if (snakemake@config$container$annotate) {
   gene2symbol <- bm[, 'external_gene_name']
   names(gene2symbol) <- bm[, snakemake@config$container$biomart$filter]
 
-  rowData_ <- data.frame(transcript_ids = sapply(ec_members, function(m) paste0(tx2gene[m, "transcript"], collapse = ",")),
+  rowData_ <- data.frame(transcript_ids = sapply(ec_members, function(m) paste0(as.character(tx2gene[m, "transcript"]), collapse = ",")),
                          gene_ids = sapply(ec2gene, function(m) paste0(m, collapse = ",")),
                          symbols = sapply(ec2gene, function(m) { paste0(unname(gene2symbol[m]), collapse = ",") }))
 } else {