D4TAlink.light - Quick start

In D4TAlink.light: GDP - Workflow Management

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

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))

D4TAlink.light documentation built on April 4, 2025, 1:02 a.m.