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D4TAlink.light - Quick start

Grégoire Thomas

October 04, 2023

  1. Load D4TAlink.light
if (!require("D4TAlink.light", quietly = TRUE)) install.packages("D4TAlink.light")
library(D4TAlink.light)
  1. Parametrise
setTaskAuthor("Doe Johns")
setTaskSponsor("myClient")
setTaskRoot("~/myDataRepository", dirCreate = TRUE)
  1. Create two tasks (package refers here to a work package)
task1 <- initTask(project = "DiseaseABC", 
                  package = "myStudy", 
                  taskname = "2022-09-01_myFirstAnalysis")
task2 <- initTask(project = "DiseaseABC", 
                  package = "myStudy", 
                  taskname = "2022-09-05_mySecondAnalysis")
  1. List the tasks in repository
print(listTasks())
  1. Load a task from the repository
mytask <- loadTask(project = "DiseaseABC", 
                  package = "myStudy", 
                  taskname = "2022-09-05_mySecondAnalysis")
  1. Add data to a task
d <- list(letters = data.frame(a = LETTERS, b = letters, c = 1:length(letters)), 
          other = data.frame(a = 1:3, b = 11:13))
saveBinary(d, mytask, "myTables")
  1. Load data from a task
e  <- readBinary(mytask, "myTables")
  1. Add reports to a task
excelfilename <- saveReportXls(d, mytask, "tables")

pdffilename <- pdfReport(mytask, "myPlot", dim = c(150, 150)) # 150mm x 150mm
plot(pi)
dev.off()

csvfile <- reportFn(mytask, "someData", "csv")
p <- data.frame(a = LETTERS, b = letters, c = 1:length(letters))
write.table(p, csvfile)
print(csvfile)
  1. Add R markdown file from template to a task
rmdfile <- initTaskRmd(mytask)
print(rmdfile)
  1. Render a task’s R markdown file
# May require having run 'tinytex::install_tinytex()'
docfile <- renderTaskRmd(mytask) 
if (require("Biobase", quietly = TRUE)) Biobase::openPDF(docfile)
  1. List content of task
print(listTaskFiles(mytask))

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.