- Fixing an error

- Destroying vignette to match bioconductor requirements
- Minor Improvements

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: cbaf
 biocViews: Technology
 Title: Multiple automated functions for cbioportal.org.
-Version: 0.99.4
+Version: 0.99.5
 Authors@R: c(person("Arman", "Shahrisa", role = c("aut", "cre", "cph"),
                      email = "shahrisa.arman@hotmail.com"),
             person("Maryam", "Tahmasebi Birgani", role = "aut",

R/cbaf-availableData.R

@@ -25,16 +25,12 @@
 #'
 #' @usage availableData(excelFileName)
 #'
-#' @param outputName a character string that is required to name the output and,
-#' if requested, excel file.
+#' @param excelFileName a character string that is required to name the output
+#' and, if requested, excel file.
 #'
-#' @param excelFile a logical value that tells the function whether or not
-#' export the results as an excel file.
-#' Default value is TRUE.
 #'
 #' @return A matrix that contains all cancer studies versus available data types
-#' . It is available as a variable with outputName. In addition, output data can
-#'  be stored as an excel file with the same output in the working directory.
+#' . It is available as an excel file with the given name.
 #'
 #'
 #'

R/cbaf-heatmapOutput.R

@@ -344,9 +344,9 @@ heatmapOutput <- function(submissionName, shortenStudyNames = TRUE, genelimit =
 
   # Create progressbar
 
-  total.number <- l
+  total.number <-
 
-  ength(statisticsData)*length((statisticsData[[1]])[
+  length(statisticsData)*length((statisticsData[[1]])[
 
     names(statisticsData[[1]]) %in% c("Frequency.Percentage", "Mean.Value",