rqcReport: Quality Control HTML Report

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

View source: R/rqcReport.R

Description

Generates an HTML report file.

Usage

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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

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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)

labbcb/Rqc documentation built on Aug. 2, 2021, 8:43 a.m.