Rqc (version 1.6.2)

rqcReport: 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.

Value

Report file path.

Details

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

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)