rqcReport: Quality Control HTML Report
In labbcb/Rqc: Quality Control Tool for High-Throughput Sequencing Data

Description Usage Arguments Details Value Author(s) See Also Examples

Generates an HTML report file.

rqcReport(
  rqcResultSet,
  outdir = tempdir(),
  file = "rqc_report",
  keepMD = FALSE,
  templateFile = system.file("templates", package = "Rqc", "rqc_report.Rmd")
)

`rqcResultSet`	list of `RqcResultSet` objects created by `rqc` and `rqcQA` functions.
`outdir`	output directory path. It is created a temporary directory by default.
`file`	output file name.
`keepMD`	If true Rqc does not delete markdown file. `knit` function takes RMarkdown template file (within package) and generates a temporary Markdown file. Next `markdownToHTML` function takes this markdown file and creates final HTML file.
`templateFile`	Path of Rmarkdown file as Rqc web report template.

Also creates a directory called "figure" in outdir path.

Report file path.

Welliton Souza

rqc

rqcQA

options(device.ask.default = FALSE)
checkpoint("Rqc", path=system.file(package="Rqc", "extdata"), {
  folder <- system.file(package="ShortRead", "extdata/E-MTAB-1147")
  files <- list.files(full.names=TRUE, path=folder)
  rqcResultSet <- rqcQA(files, pair=c(1,1), workers=1)
}, keep="rqcResultSet")
reportFile <- rqcReport(rqcResultSet)
browseURL(reportFile)