tests/FastqDataSet,reports,qrqc,future.R

In HenrikBengtsson/aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

library("aroma.seq")

fullTest <- (Sys.getenv("_R_CHECK_FULL_") != "")
fullTest <- fullTest && require("qrqc")

# Setup (writable) local data directory structure
setupExampleData()

dataSet <- "TopHat-example"
organism <- "Lambda_phage"

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# Setup FASTQ set
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fqs <- FastqDataSet$byName(dataSet, organism=organism, paired=FALSE)
print(fqs)

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# Generate QC report
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if (fullTest) {
  html <- report(fqs, verbose=-10)
  print(html)
}