rqcReport {Rqc}R Documentation

Quality Control HTML Report

Description

Generates an HTML report file.

Usage

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

Arguments

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.

Details

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

Value

Report file path.

Author(s)

Welliton Souza

See Also

rqc

rqcQA

Examples


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)
[Package Rqc version 1.16.2 Index]