@@ -278,7 +278,7 @@ Reference: [TCGA wiki](https://wiki.nci.nih.gov/display/TCGA/Microsatellite+data

 Level 3 data is included in BCR clinical-based submissions and can be downloaded as follows:

-```{r results = 'hide', echo=TRUE, message=FALSE, warning=FALSE,eval = F}

+```{r msi, results = 'hide', echo=TRUE, message=FALSE, warning=FALSE,eval = F}

 query <- GDCquery(

     project = "TCGA-COAD", 

     data.category = "Other",

@@ -290,6 +290,7 @@ query <- GDCquery(

 GDCdownload(query)

 msi_results <- GDCprepare_clinic(query, "msi")

 ```

+

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

 msi_results %>% DT::datatable(options = list(scrollX = TRUE, keys = TRUE))

 ```

@@ -308,19 +309,19 @@ query_legacy <- GDCquery(

 ) 

 # Tissue slide image files from harmonized database

-query.harmonized <- GDCquery(

+query_harmonized <- GDCquery(

     project = "TCGA-OV",

     data.category = "Biospecimen",

     data.type = 'Slide Image'

 )

 ```

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

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

 query_legacy %>% 

     getResults %>% 

     DT::datatable(options = list(scrollX = TRUE, keys = TRUE))

-query.harmonized  %>% 

+query_harmonized  %>% 

     getResults %>% 

     head  %>% 

     DT::datatable(options = list(scrollX = TRUE, keys = TRUE))

@@ -330,7 +331,7 @@ query.harmonized  %>%

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

 # Pathology report from harmonized portal 

-query.harmonized <- GDCquery(

+query_harmonized <- GDCquery(

     project = "TCGA-COAD", 

     data.category = "Biospecimen", 

     data.type = "Slide Image",

@@ -339,8 +340,8 @@ query.harmonized <- GDCquery(

 )  

 ```

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

-query.harmonized  %>% 

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

+query_harmonized  %>% 

     getResults %>% 

     head  %>% 

     DT::datatable(options = list(scrollX = TRUE, keys = TRUE))

@@ -415,7 +416,7 @@ query %>%

 ## Clinical data (Biotab format)

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

+```{r biotab_legacy,results = 'hide', echo=TRUE, message=FALSE, warning=FALSE}

 # Clinical data

 query <- GDCquery(

     project = "TCGA-COAD", 

@@ -435,12 +436,12 @@ query %>%

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

 GDCdownload(query)

-clinical.biotab <- GDCprepare(query)

+clinical_biotab <- GDCprepare(query)

 ```

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

-names(clinical.biotab)

-datatable(clinical.biotab$clinical_radiation_coad, options = list(scrollX = TRUE, keys = TRUE))

+names(clinical_biotab)

+datatable(clinical_biotab$clinical_radiation_coad, options = list(scrollX = TRUE, keys = TRUE))

 ```

 # Filter functions