Merge branch 'master' of github.com:BioinformaticsFMRP/TCGAbiolinks

vignettes/tcgaBiolinks.Rmd

@@ -456,17 +456,39 @@ with the following arguments:
 The next subsections will detail each of the search arguments.
 Below, we show some search examples:
 ```{r, eval = FALSE}
+#---------------------------------------------------------------
+#  For available entries and combinations please se table below
+#---------------------------------------------------------------
+
+# Gene expression aligned against Hg38
 query <- GDCquery(project = "TARGET-AML",
                   data.category = "Transcriptome Profiling",
                   data.type = "Gene Expression Quantification", 
                   workflow.type = "HTSeq - Counts")
 
-# Using legacy
+
+# Using sample type to get only Primary solid Tumor samples and Solid Tissue Normal
+query.mirna <- GDCquery(project = "TCGA-ACC", 
+                        data.category = "Transcriptome Profiling", 
+                        data.type = "miRNA Expression Quantification",
+                        sample.type = c("Primary solid Tumor","Solid Tissue Normal"))
+
+# Example Using legacy to accessing hg19 and filtering by barcode
 query <- GDCquery(project = "TCGA-GBM",
                   data.category = "DNA methylation", 
                   platform = "Illumina Human Methylation 27", 
                   legacy = TRUE,
                   barcode = c("TCGA-02-0047-01A-01D-0186-05","TCGA-06-2559-01A-01D-0788-05"))
+
+# Gene expression aligned against hg19.
+query.exp.hg19 <- GDCquery(project = "TCGA-GBM",
+                  data.category = "Gene expression",
+                  data.type = "Gene expression quantification",
+                  platform = "Illumina HiSeq", 
+                  file.type  = "normalized_results",
+                  experimental.strategy = "RNA-Seq",
+                  barcode = c("TCGA-14-0736-02A-01R-2005-01", "TCGA-06-0211-02A-02R-2005-01"),
+                  legacy = TRUE)
 ```
 
 The list of projects is below: