R/RenderReport.R

In SeqSQC: A bioconductor package for sample quality check with next generation sequencing data

#' Render the rmarkdown file for generating a sample QC report.
#' 
#' Function to render the pre-compiled rmarkdown file to generate the
#' sample QC report.
#' @param input SeqSQC object with QC results.
#' @param output a character string to define the file name for the QC
#'     report.
#' @param interactive whether to generate interative plots in the
#'     report. The default is TRUE.
#' @importFrom rmarkdown render
#' @return Will incure the rendering of the rmarkdown file for
#'     generating the sample QC report. The report will return to the
#'     file denoted in \code{output} in the function.
#' @export
#' @author Qian Liu \email{qliu7@@buffalo.edu}
#' @examples
#' load(system.file("extdata", "example.seqfile.Rdata", package="SeqSQC"))
#' RenderReport(seqfile, output="report.html", interactive=FALSE)

RenderReport <- function(input, output, interactive = TRUE){
    report <- system.file("extdata", "sampleQCReport.Rmd", package="SeqSQC")
    render(report,
           output_file = basename(output),
           output_dir=dirname(output),
           params=list(
               seqfile = input,
               interactive = interactive
           ))
}