Write an HTML Summary Report — writeHtmlReport • ngsReports

Compiles an HTML report using a supplied template

writeHtmlReport(
  fastqcDir,
  template,
  outDir,
  usePlotly = TRUE,
  species = "Hsapiens",
  gcType = c("Genome", "Transcriptome"),
  nOver = 30,
  targetsDF,
  overwrite = FALSE,
  quiet = TRUE
)

Arguments

fastqcDir: A directory containing zipped, or extracted FastQC reports
template: The template file which will be copied into fastqcDir
outDir: The directory to write the compiled document to
usePlotly: Generate interactive plots?
species: Species/closely related species of sequenced samples
gcType: Is the data "Transcriptomic" or "Genomic" in nature?
nOver: The maximum number of Overrepresented Sequences to show
targetsDF: A data.frame with at least two columns named Filename and Label. The filenames should match the original fastq files, and the labels should be simply alternative labels for these files for convenience.
overwrite: logical. Overwrite any previous copies of the template file in the destination directory
quiet: logical. Show or hide markdown output in the Console.

Value

Silently returns TRUE and will output a compiled HTML file from the supplied Rmarkdown template file

Details

This will take a user supplied template, or the file supplied with the package and create an HTML summary of all standard FASTQC plots for all files in the supplied directory.

Examples

if (FALSE) { # \dontrun{
packageDir <- system.file("extdata", package = "ngsReports")
fileList <- list.files(packageDir, pattern = "fastqc.zip", full.names= TRUE)
# Copy these files to tempdir() to avoid overwriting
# any files in the package directory
file.copy(fileList, tempdir(), overwrite = TRUE)
writeHtmlReport(fastqcDir = tempdir())
} # }