D4TAlink.light - Quick start

Grégoire Thomas

November 29, 2024

  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))