Merge pull request #582 from BioinformaticsFMRP/devel

Devel
BioinformaticsFMRP · May 22, 2023 · 5bc64a8 · 5bc64a8
2 parents 56af0fc + 3b51a98
commit 5bc64a8
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: TCGAbiolinks
 Type: Package
 Title: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
-Version: 2.29.0
+Version: 2.29.3
 Date: 2022-17-08
 Author: Antonio Colaprico,
     Tiago Chedraoui Silva,

diff --git a/NAMESPACE b/NAMESPACE
@@ -109,6 +109,7 @@ importFrom(dplyr,mutate_all)
 importFrom(dplyr,pull)
 importFrom(dplyr,row_number)
 importFrom(dplyr,slice)
+importFrom(dplyr,summarise)
 importFrom(grDevices,dev.list)
 importFrom(grDevices,dev.off)
 importFrom(grDevices,pdf)

diff --git a/NEWS b/NEWS
@@ -1,3 +1,9 @@
+CHANGES IN VERSION 2.29.1
+-------------------------
+
+* Removing support to legacy archive since it will be shutdown by GDC soon.
+* When saving files we will not include folders prefix  legacy/harmonized anymore
+
 CHANGES IN VERSION 2.21.1
 -------------------------
 
@@ -27,16 +33,16 @@ CHANGES IN VERSION 2.7.13
 CHANGES IN VERSION 2.5.0
 -------------------------
 
-Changing chunks.per.download to files.per.chunk
+* Changing chunks.per.download to files.per.chunk
 
 CHANGES IN VERSION 2.2.0
 -------------------------
 
 NEW FEATURES
-    o Add GISTIC2 information and Mutation information in the summarizedExperiment while preparing GDC data
+* Add GISTIC2 information and Mutation information in the summarizedExperiment while preparing GDC data
 
 SIGNIFICANT USER-LEVEL CHANGES
-    o Speed up GDCquery
+* Speed up GDCquery
 
 TCGAbiolinks 2.0
 ---------------------------------------------------------------

diff --git a/R/analyze.R b/R/analyze.R
@@ -1987,59 +1987,33 @@ getAdjacencyBiogrid <- function(tmp.biogrid, names.genes = NULL) {
 #' DNA methylation and Gene expression data from GDC database
 #' @param project A GDC project
 #' @param n Number of samples to return. If NULL return all (default)
-#' @param legacy Access legacy (hg19) or harmonized database (hg38).
 #' @return A vector of barcodes
 #' @export
 #' @examples
 #' # Get ACC samples with both  DNA methylation (HM450K) and gene expression aligned to hg19
-#' samples <- matchedMetExp("TCGA-UCS", legacy = TRUE)
+#' samples <- matchedMetExp("TCGA-UCS")
 matchedMetExp <- function(
         project,
-        legacy = FALSE,
         n = NULL
 ) {
-    if (legacy) {
-        # get primary solid tumor samples: DNA methylation
-        message("Download DNA methylation information")
-        met450k <- GDCquery(
-            project = project,
-            data.category = "DNA methylation",
-            platform = "Illumina Human Methylation 450",
-            legacy = TRUE,
-            sample.type = c("Primary Tumor")
-        )
-
-        # get primary solid tumor samples: RNAseq
-        message("Download gene expression information")
-        exp <- GDCquery(
-            project = project,
-            data.category = "Gene expression",
-            data.type = "Gene expression quantification",
-            platform = "Illumina HiSeq",
-            file.type  = "results",
-            sample.type = c("Primary Tumor"),
-            legacy = TRUE
-        )
-    } else {
-        # get primary solid tumor samples: DNA methylation
-        message("Download DNA methylation information")
-        met450k <- GDCquery(
-            project = project,
-            data.category = "DNA Methylation",
-            platform = "Illumina Human Methylation 450",
-            sample.type = c("Primary Tumor")
-        )
 
-        # get primary solid tumor samples: RNAseq
-        message("Download gene expression information")
-        exp <- GDCquery(
-            project = project,
-            data.category = "Transcriptome Profiling",
-            data.type = "Gene Expression Quantification",
-            workflow.type = "STAR - Counts"
-        )
+    # get primary solid tumor samples: DNA methylation
+    message("Download DNA methylation information")
+    met450k <- GDCquery(
+        project = project,
+        data.category = "DNA Methylation",
+        platform = "Illumina Human Methylation 450",
+        sample.type = c("Primary Tumor")
+    )
 
-    }
+    # get primary solid tumor samples: RNAseq
+    message("Download gene expression information")
+    exp <- GDCquery(
+        project = project,
+        data.category = "Transcriptome Profiling",
+        data.type = "Gene Expression Quantification",
+        workflow.type = "STAR - Counts"
+    )
 
     # Get patients with samples in both platforms
     met450k_tp <- met450k$results[[1]]$cases