writeHtmlReport: Write an HTML Summary Report

In steveped/ngsReports: Load FastqQC reports and other NGS related files

Write an HTML Summary Report

Description

Compiles an HTML report using a supplied template

Usage

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.

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.

Value

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

Examples

## Not run: 
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())

## End(Not run)

steveped/ngsReports documentation built on May 9, 2024, 10:07 a.m.