Update

Author: tiagochst

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: TCGAWorkflow
 Title: TCGA Workflow Analyze cancer genomics and epigenomics data using
     Bioconductor packages
-Version: 1.17.3
+Version: 1.17.4
 Workflow: True
 Author: Tiago Chedraoui Silva  <tiagochst@gmail.com>,
     Antonio Colaprico <antonio.colaprico@ulb.ac.be>,

vignettes/TCGAWorkflow.Rmd

@@ -832,14 +832,14 @@ one or more selected chromosomes.
 LGGmut <- GDCquery_Maf(tumor = "LGG", pipelines = "mutect2")
 ```
 
-```{r results='hide', echo=TRUE, message=FALSE,warning=FALSE}
+```{r results='hide', echo=TRUE, message=FALSE,warning=TRUE, eval = FALSE}
 ###############################################
 ## Genomic aberration overview - Circos plot ## 
 ###############################################
 # Retrieve curated mutations for selected cancer (e.g. "LGG") 
 data(mafMutect2LGGGBM)
 # Select only potentially damaging mutations
-LGGmut %>% 
+LGGmut <- LGGmut %>% 
   dplyr::filter(
     Variant_Classification %in% 
       c(
@@ -876,10 +876,12 @@ names(colors)  <- c(0,1)
 colors <- c("blue","green","red","gold")
 names(colors)  <- typeNames[1:4]
 circos.genomicTrackPlotRegion(
-  s.mut, ylim = c(1.2,4.2),
+  s.mut, 
+  ylim = c(1.2,4.2),
   panel.fun = function(region, value, ...) {
     circos.genomicPoints(region, value, cex = 0.8, pch = 16, col = colors[value[[2]]], ...)
-  })
+  }
+)
 
 circos.clear()