@@ -6,19 +6,19 @@ vignette: >

     %\VignetteEngine{knitr::rmarkdown}

     \usepackage[utf8]{inputenc}

 ---

-  

+

 ```{r setup, include=FALSE}

 knitr::opts_chunk$set(dpi = 300)

 knitr::opts_chunk$set(cache=FALSE)

 ```

-  

+

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

 library(TCGAbiolinks)

 library(SummarizedExperiment)

 library(dplyr)

 library(DT)

 ```

-  

+

 TCGAbiolinks retrieved molecular subtypes information from TCGA samples.

 The functions `PanCancerAtlas_subtypes` and `TCGAquery_subtype` can be used to get the information tables.

@@ -34,10 +34,12 @@ Synapse has published a single file with all available molecular subtypes that h

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

 subtypes <- PanCancerAtlas_subtypes()

-DT::datatable(subtypes,

-             filter = 'top',

-             options = list(scrollX = TRUE, keys = TRUE, pageLength = 5),

-             rownames = FALSE)

+DT::datatable(

+    data = subtypes,

+    filter = 'top',

+    options = list(scrollX = TRUE, keys = TRUE, pageLength = 5),

+    rownames = FALSE

+)

 ```

 The columns "Subtype_Selected" was selected as most prominent subtype classification (from the other columns)

@@ -105,18 +107,18 @@ These subtypes will be automatically added in the summarizedExperiment

 object through GDCprepare. But you can also use the `TCGAquery_subtype` function

 to retrieve this information.

-```{r, eval = FALSE}

+```{r, eval = TRUE}

 lgg.gbm.subtype <- TCGAquery_subtype(tumor = "lgg")

 ```

 A subset of the LGG subytpe is shown below:

 ```{r, eval = TRUE, echo = FALSE}

 datatable(

-  lgg.gbm.subtype[1:10,],

-  caption = "Table with LGG molecular subtypes from TCGAquery_subtype",

-  filter = 'top',

-  options = list(scrollX = TRUE, keys = TRUE, pageLength = 5), 

-  rownames = FALSE

+    lgg.gbm.subtype[1:10,],

+    caption = "Table with LGG molecular subtypes from TCGAquery_subtype",

+    filter = 'top',

+    options = list(scrollX = TRUE, keys = TRUE, pageLength = 5), 

+    rownames = FALSE

 )

 ```