@@ -64,7 +64,7 @@ Other useful clinical information available are:

 ## Clinical

 In this example we will fetch clinical data from  BCR Biotab files.

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

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

 query <- GDCquery(

     project = "TCGA-ACC", 

     data.category = "Clinical",

@@ -94,37 +94,27 @@ clinical.BCRtab.all$clinical_drug_acc  %>%

 ```

-In this example we will fetch all BRCA BCR Biotab files, and look for the ER status.

+In this example we will fetch all ACC BCR Biotab files, and look for the ER status.

 ```{r, results = "hide",cache=TRUE, message=FALSE}

 library(TCGAbiolinks)

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

-                  data.category = "Clinical",

-                  data.type = "Clinical Supplement", 

-                  data.format = "BCR Biotab")

+query <- GDCquery(

+    project = "TCGA-ACC", 

+    data.category = "Clinical",

+    data.type = "Clinical Supplement", 

+    data.format = "BCR Biotab"

+)

+

 GDCdownload(query)

-clinical.BCRtab.all <- GDCprepare(query)

+clinical_tab_all <- GDCprepare(query)

 ```

 ```{R}

 # All available tables

-names(clinical.BCRtab.all)

-

-# colnames from clinical_patient_brca

-tibble::tibble(sort(colnames(clinical.BCRtab.all$clinical_patient_brca)))

+names(clinical_tab_all)

-# ER status count

-plyr::count(clinical.BCRtab.all$clinical_patient_brca$er_status_by_ihc)

-

-# ER content 

-er.cols <- grep("^er",colnames(clinical.BCRtab.all$clinical_patient_brca))

-clinical.BCRtab.all$clinical_patient_brca[,c(2,er.cols)] %>% 

-    DT::datatable(options = list(scrollX = TRUE))

-

-# All columns content first rows

-clinical.BCRtab.all$clinical_patient_brca %>% 

-    head  %>% 

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

+# columns from clinical_patient

+dplyr::glimpse(clinical_tab_all$clinical_patient_acc)

 ```

 ## Biospecimen

@@ -132,19 +122,21 @@ clinical.BCRtab.all$clinical_patient_brca %>%

 ```{r, results = "hide",cache=TRUE, message=FALSE,warning=FALSE}

 # Biospecimen BCR Biotab

-query.biospecimen <- GDCquery(project = "TCGA-BRCA", 

-                              data.category = "Biospecimen",

-                              data.type = "Biospecimen Supplement", 

-                              data.format = "BCR Biotab")

-GDCdownload(query.biospecimen)

-biospecimen.BCRtab.all <- GDCprepare(query.biospecimen)

+query_biospecimen <- GDCquery(

+    project = "TCGA-ACC", 

+    data.category = "Biospecimen",

+    data.type = "Biospecimen Supplement", 

+    data.format = "BCR Biotab"

+)

+GDCdownload(query_biospecimen)

+biospecimen_tab_all <- GDCprepare(query_biospecimen)

 ```

 ```{R}

 # All available tables

-names(biospecimen.BCRtab.all)

+names(biospecimen_tab_all)

-biospecimen.BCRtab.all$ssf_normal_controls_ov  %>% 

+biospecimen_tab_all$biospecimen_sample_acc  %>% 

     head  %>% 

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

 ```

@@ -155,53 +147,35 @@ biospecimen.BCRtab.all$ssf_normal_controls_ov  %>%

 In this example we will fetch clinical indexed data (same as showed in the data portal).

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

-clinical <- GDCquery_clinic(project = "TCGA-LUAD", type = "clinical")

+clinical <- GDCquery_clinic(project = "TCGA-ACC", type = "clinical")

 ```

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

 clinical %>%

     head %>% 

-    DT::datatable(filter = 'top', 

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

-                  rownames = FALSE)

-```

-

-

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

-clinical <- GDCquery_clinic(project = "BEATAML1.0-COHORT", type = "clinical")

-```

-

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

-clinical %>% 

-    head %>% 

-    DT::datatable(filter = 'top', 

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

-                  rownames = FALSE)

+    DT::datatable(

+        filter = 'top', 

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

+        rownames = FALSE

+    )

 ```

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

-clinical <- GDCquery_clinic(project = "CPTAC-2", type = "clinical")

-```

-

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

-clinical %>% 

-    head %>% 

-    DT::datatable(filter = 'top', 

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

-                  rownames = FALSE)

-```

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

+clinical_beataml <- GDCquery_clinic(

+    project = "BEATAML1.0-COHORT", 

+    type = "clinical"

+)

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

-clinical <- GDCquery_clinic(project = "GENIE-MSK", type = "clinical")

-```

+clinical_cptac2 <- GDCquery_clinic(

+    project = "CPTAC-2", 

+    type = "clinical"

+)

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

-clinical %>% 

-    head %>% 

-    DT::datatable(filter = 'top', 

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

-                  rownames = FALSE)

+clinical_genie <- GDCquery_clinic(

+    project = "GENIE-MSK", 

+    type = "clinical"

+)

 ```

@@ -242,22 +216,27 @@ The selection of the table is done by the argument `clinical.info`.

 Below are several examples fetching clinical data directly from the clinical XML files.

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

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

-                  data.category = "Clinical", 

-                  file.type = "xml", 

-                  barcode = c("TCGA-RU-A8FL","TCGA-AA-3972"))

+query <- GDCquery(

+    project = "TCGA-COAD", 

+    data.category = "Clinical", 

+    file.type = "xml", 

+    barcode = c("TCGA-RU-A8FL","TCGA-AA-3972")

+)

 GDCdownload(query)

 clinical <- GDCprepare_clinic(query, clinical.info = "patient")

 ```

+

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

 clinical %>% 

     datatable(filter = 'top', 

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

               rownames = FALSE)

 ```

+

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

 clinical.drug <- GDCprepare_clinic(query, clinical.info = "drug")

 ```

+

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

 clinical.drug %>% 

     datatable(filter = 'top', 

@@ -268,15 +247,18 @@ clinical.drug %>%

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

 clinical.radiation <- GDCprepare_clinic(query, clinical.info = "radiation")

 ```

+

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

 clinical.radiation %>% 

     datatable(filter = 'top', 

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

               rownames = FALSE)

 ```

+

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

 clinical.admin <- GDCprepare_clinic(query, clinical.info = "admin")

 ```

+

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

 clinical.admin %>% 

     datatable(filter = 'top', 

@@ -297,12 +279,14 @@ 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}

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

-                  data.category = "Other",

-                  legacy = TRUE,

-                  access = "open",

-                  data.type = "Auxiliary test",

-                  barcode = c("TCGA-AD-A5EJ","TCGA-DM-A0X9"))  

+query <- GDCquery(

+    project = "TCGA-COAD", 

+    data.category = "Other",

+    legacy = TRUE,

+    access = "open",

+    data.type = "Auxiliary test",

+    barcode = c("TCGA-AD-A5EJ","TCGA-DM-A0X9")

+)  

 GDCdownload(query)

 msi_results <- GDCprepare_clinic(query, "msi")

 ```

@@ -315,20 +299,24 @@ msi_results %>% DT::datatable(options = list(scrollX = TRUE, keys = TRUE))

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

 # Tissue slide image files from legacy database

-query.legacy <- GDCquery(project = "TCGA-COAD", 

-                         data.category = "Clinical", 

-                         data.type = "Tissue slide image",

-                         legacy = TRUE,

-                         barcode = c("TCGA-RU-A8FL","TCGA-AA-3972")) 

+query_legacy <- GDCquery(

+    project = "TCGA-COAD", 

+    data.category = "Clinical", 

+    data.type = "Tissue slide image",

+    legacy = TRUE,

+    barcode = c("TCGA-RU-A8FL","TCGA-AA-3972")

+) 

 # Tissue slide image files from harmonized database

-query.harmonized <- GDCquery(project = "TCGA-OV",

-                             data.category = "Biospecimen",

-                             data.type = 'Slide Image')

+query.harmonized <- GDCquery(

+    project = "TCGA-OV",

+    data.category = "Biospecimen",

+    data.type = 'Slide Image'

+)

 ```

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

-query.legacy %>% 

+query_legacy %>% 

     getResults %>% 

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

@@ -342,11 +330,13 @@ query.harmonized  %>%

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

 # Pathology report from harmonized portal 

-query.harmonized <- GDCquery(project = "TCGA-COAD", 

-                             data.category = "Biospecimen", 

-                             data.type = "Slide Image",

-                             experimental.strategy = "Diagnostic Slide",

-                             barcode = c("TCGA-RU-A8FL","TCGA-AA-3972"))  

+query.harmonized <- GDCquery(

+    project = "TCGA-COAD", 

+    data.category = "Biospecimen", 

+    data.type = "Slide Image",

+    experimental.strategy = "Diagnostic Slide",

+    barcode = c("TCGA-RU-A8FL","TCGA-AA-3972")

+)  

 ```

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

@@ -370,15 +360,17 @@ The clinical data types available in legacy database are:

 ## Pathology report (PDF)

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

 # Pathology report from legacy portal 

-query.legacy <- GDCquery(project = "TCGA-COAD", 

-                         data.category = "Clinical", 

-                         data.type = "Pathology report",

-                         legacy = TRUE,

-                         barcode = c("TCGA-RU-A8FL","TCGA-AA-3972"))  

+query_legacy <- GDCquery(

+    project = "TCGA-COAD", 

+    data.category = "Clinical", 

+    data.type = "Pathology report",

+    legacy = TRUE,

+    barcode = c("TCGA-RU-A8FL","TCGA-AA-3972")

+)  

 ```

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

-query.legacy %>% 

+query_legacy %>% 

     getResults %>% 

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

 ```

@@ -387,11 +379,13 @@ query.legacy %>%

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

 # Tissue slide image

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

-                  data.category = "Clinical", 

-                  data.type = "Tissue slide image",

-                  legacy = TRUE,

-                  barcode = c("TCGA-RU-A8FL","TCGA-AA-3972")) 

+query <- GDCquery(

+    project = "TCGA-COAD", 

+    data.category = "Clinical", 

+    data.type = "Tissue slide image",

+    legacy = TRUE,

+    barcode = c("TCGA-RU-A8FL","TCGA-AA-3972")

+) 

 ```

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

@@ -404,11 +398,13 @@ query %>%

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

 # Clinical Supplement

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

-                  data.category = "Clinical", 

-                  data.type = "Clinical Supplement",

-                  legacy = TRUE,

-                  barcode = c("TCGA-RU-A8FL","TCGA-AA-3972")) 

+query <- GDCquery(

+    project = "TCGA-COAD", 

+    data.category = "Clinical", 

+    data.type = "Clinical Supplement",

+    legacy = TRUE,

+    barcode = c("TCGA-RU-A8FL","TCGA-AA-3972")

+) 

 ```

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

@@ -421,11 +417,13 @@ query %>%

 ## Clinical data (Biotab format)

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

 # Clinical data

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

-                  data.category = "Clinical", 

-                  data.type = "Clinical data",

-                  legacy = TRUE,

-                  file.type = "txt")  

+query <- GDCquery(

+    project = "TCGA-COAD", 

+    data.category = "Clinical", 

+    data.type = "Clinical data",

+    legacy = TRUE,

+    file.type = "txt"

+)  

 ```

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

@@ -498,7 +496,8 @@ bar <- c("TCGA-G9-6378-02A-11R-1789-07", "TCGA-CH-5767-04A-11R-1789-07",

          "TCGA-B6-A1KN-60A-13R-1789-07", "TCGA-AO-A0J5-01A-11R-1789-07",

          "TCGA-AO-A0J5-01A-11R-1789-07", "TCGA-G9-6336-11A-11R-1789-07",

          "TCGA-G9-6380-11A-11R-1789-07", "TCGA-G9-6380-01A-11R-1789-07",

-         "TCGA-G9-6340-01A-11R-1789-07", "TCGA-G9-6340-11A-11R-1789-07")

+         "TCGA-G9-6340-01A-11R-1789-07", "TCGA-G9-6340-11A-11R-1789-07"

+)

 S <- TCGAquery_SampleTypes(bar,"TP")

 S2 <- TCGAquery_SampleTypes(bar,"NB")