changed signature for curatedTCGAData() call to include version

BaderLab · Dec 9, 2020 · 0821371 · 0821371
1 parent fdf09a0
commit 0821371
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Showing 7 changed files with 43 additions and 14 deletions.
diff --git a/R/buildPredictor.R b/R/buildPredictor.R
@@ -95,10 +95,10 @@
 #'
 #' library(curatedTCGAData)
 #' library(MultiAssayExperiment)
-#' curatedTCGAData(diseaseCode="BRCA", assays="*",dry.run=TRUE)
+#' curatedTCGAData(diseaseCode="BRCA", assays="*",dry.run=TRUE,version="1.1.38")
 #' 
 #' # fetch mrna, mutation data
-#' brca <- curatedTCGAData("BRCA",c("mRNAArray"),FALSE)
+#' brca <- curatedTCGAData("BRCA",c("mRNAArray"),FALSE,version="1.1.38")
 #' 
 #' # get subtype info
 #' pID <- colData(brca)$patientID

diff --git a/R/createPSN_MultiData.R b/R/createPSN_MultiData.R
@@ -25,10 +25,10 @@
 #'
 #' library(curatedTCGAData)
 #' library(MultiAssayExperiment)
-#' curatedTCGAData(diseaseCode='BRCA', assays='*',dry.run=TRUE)
+#' curatedTCGAData(diseaseCode='BRCA', assays='*',dry.run=TRUE,version="1.1.38")
 #' 
 #' # fetch mrna, mutation data
-#' brca <- curatedTCGAData('BRCA',c('mRNAArray'),FALSE)
+#' brca <- curatedTCGAData('BRCA',c('mRNAArray'),FALSE,version="1.1.38")
 #' 
 #' # get subtype info
 #' pID <- colData(brca)$patientID

diff --git a/man/buildPredictor.Rd b/man/buildPredictor.Rd
diff --git a/man/createPSN_MultiData.Rd b/man/createPSN_MultiData.Rd
diff --git a/man/replacePattern.Rd b/man/replacePattern.Rd
diff --git a/vignettes/BuildPredictor.Rmd b/vignettes/BuildPredictor.Rmd
@@ -19,7 +19,8 @@ suppressWarnings(suppressMessages(require(netDx)))
 suppressWarnings(suppressMessages(library(curatedTCGAData)))
 
 # fetch data remotely
-brca <- suppressMessages(curatedTCGAData("BRCA",c("mRNAArray"),FALSE))
+brca <- suppressMessages(curatedTCGAData("BRCA",c("mRNAArray"),FALSE,
+	version="1.1.38"))
 
 # process input variables
 staget <- sub("[abcd]","",sub("t","",colData(brca)$pathology_T_stage))
@@ -241,12 +242,14 @@ suppressMessages(library(curatedTCGAData))
 
 Take a look at the available data without downloading any:
 ```{r,eval=TRUE}
-curatedTCGAData(diseaseCode="BRCA", assays="*",dry.run=TRUE)
+curatedTCGAData(diseaseCode="BRCA", assays="*",dry.run=TRUE,
+	version="1.1.38")
 ```
 
 We will work only with the mRNA data in this example:
 ```{r,eval=TRUE}
-brca <- suppressMessages(curatedTCGAData("BRCA",c("mRNAArray"),FALSE))
+brca <- suppressMessages(curatedTCGAData("BRCA",c("mRNAArray"),FALSE,
+	version="1.1.38"))
 ```
 
 This next code block prepares the TCGA data. In practice you would do this once, and save the data before running netDx, but we run it here to see an end-to-end example. 

diff --git a/vignettes/ThreeWayClassifier.Rmd b/vignettes/ThreeWayClassifier.Rmd
@@ -22,7 +22,7 @@ suppressWarnings(suppressMessages(library(curatedTCGAData)))
 brca <- suppressMessages(
    curatedTCGAData("BRCA",
                c("mRNAArray","RPPA*","Methylation_methyl27*"),
-	dry.run=FALSE))
+	dry.run=FALSE,version="1.1.38"))
 
 # process input variables
 # prepare clinical variable - stage
@@ -168,7 +168,7 @@ suppressMessages(library(curatedTCGAData))
 
 We use the `curatedTCGAData()` command to look at available assays in the breast cancer dataset. 
 ```{r,eval=TRUE}
-curatedTCGAData(diseaseCode="BRCA", assays="*",dry.run=TRUE)
+curatedTCGAData(diseaseCode="BRCA", assays="*",dry.run=TRUE,version="1.1.38")
 ```
 
 In this call we fetch only the gene expression, proteomic and methylation data; setting `dry.run=FALSE` initiates the fetching of the data.
@@ -177,7 +177,7 @@ In this call we fetch only the gene expression, proteomic and methylation data;
 brca <- suppressMessages(
    curatedTCGAData("BRCA",
                c("mRNAArray","RPPA*","Methylation_methyl27*"),
-	dry.run=FALSE))
+	dry.run=FALSE,version="1.1.38"))
 ```
 
 This next code block prepares the TCGA data. In practice you would do this once, and save the data before running netDx, but we run it here to see an end-to-end example.