renderReport {systemPipeR}R Documentation

Render RMarkdown Report

Description

Render the input file to the specified output format using pandoc.

Usage

renderReport(sysargslist, type = c("html_document"),  silent = FALSE)

Arguments

sysargslist

object of class SYSargsList.

type

The R Markdown output format to convert to. Default is "ALL".The option can be the name of a format (e.g. "pdf_document" or "html_document").

silent

If set to TRUE, all messages returned by the function will be suppressed.

Value

It will return an SYSargsList updated.

Author(s)

Daniela Cassol and Thomas Girke

See Also

See also as SYSargsList-class.

Examples

## Not run: 
## Construct SYSargsList object from Rmd file
library(systemPipeRdata)
script <- system.file("extdata/workflows/rnaseq", "systemPipeRNAseq.Rmd", package="systemPipeRdata")
targets <- system.file("extdata", "targets.txt", package="systemPipeR")
dir_path <- tempdir()
SYSconfig <- initProject(projPath=dir_path, targets=targets, script=script, overwrite = TRUE)
sysargslist <- initWF(sysconfig ="SYSconfig.yml")
sysargslist <- configWF(x=sysargslist, input_steps = "1:3")
sysargslist <- runWF(sysargslist = sysargslist, steps = "ALL")
renderReport(x=sysargslist)

## End(Not run)

[Package systemPipeR version 1.26.3 Index]