evalCode: Toggles option 'eval' on the RMarkdown files

In systemPipeR: systemPipeR: NGS workflow and report generation environment

Description

Function to evaluate (eval=TRUE) or not evaluate (eval=FALSE) R chunk codes in the Rmarkdown file. This function does not run the code, just toggles between TRUE or FALSE the option eval and writes out a new file with the chosen option.

Usage

evalCode(infile, eval = TRUE, output)

Arguments

infile	name and path of the infile file, format Rmd.
eval	whether to evaluate the code and include its results. The default is TRUE.
output	name and path of the output file. File format Rmd.

Value

Writes Rmarkdown file containing the exact copy of the infile file with the option choose on the eval argument. It will be easy to toggle between run all the R chunk codes or not.

Author(s)

Daniela Cassol

Examples

## Not run: 
library(systemPipeRdata)
file <- system.file("extdata/workflows/rnaseq", "systemPipeRNAseq.Rmd", package="systemPipeRdata")
evalCode(infile=file, eval=FALSE, output="test.Rmd")
 
## End(Not run)

systemPipeR documentation built on Jan. 26, 2021, 2 a.m.