@@ -12,7 +12,7 @@ knitr::opts_chunk$set(cache = FALSE)

 ```

 ```{r, echo = FALSE,hide=TRUE, message=FALSE,warning=FALSE}

-devtools::load_all(".")

+library(TCGAbiolinks)

 ```

 ```{r message=FALSE, warning=FALSE, include=FALSE}

@@ -54,11 +54,13 @@ In this example we will retrieve two samples from TCGA and classify them expecti

 the same result as the paper.

 ```{r, eval = FALSE, message = FALSE, results = "hide"}

-query <- GDCquery(project = "TCGA-GBM",

-                   data.category = "DNA methylation",

-                   barcode = c("TCGA-06-0122","TCGA-14-1456"),

-                   platform = "Illumina Human Methylation 27",

-                   legacy = TRUE)

+query <- GDCquery(

+  project = "TCGA-GBM",

+  data.category = "DNA methylation",

+  barcode = c("TCGA-06-0122","TCGA-14-1456"),

+  platform = "Illumina Human Methylation 27",

+  legacy = TRUE

+)

 GDCdownload(query)

 data.hg19 <- GDCprepare(query)

 ```