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Read configuration file and render R Markdown document

Source: R/render_report.R
render_report.Rd

This function reads a configuration file in YAML format, extracts the parameters, and renders an R Markdown document using the specified parameters.

Usage

render_report(
  config_filepath,
  output_file = "./MutSeqR_Summary_Report.html",
  output_format = "html_document"
)

Arguments

config_filepath

The path to the configuration file.

output_file

The name of the output file. Will be saved to the outputdir in config params.

output_format

The format of the output file. Options are "html_document" (default), "pdf_document", or "all".

Value

A rendered R Markdown document.

Examples

# Step 1: Copy the example configuration file to your working directory
## config <- system.file("extdata", "inputs", "summary_config.yaml", package = "MutSeqR")
## file.copy(from = config, to = "your/working/directory/summary_config.yaml")
# Step 2: Edit the configuration file with your inputs
# Step 3: Render the report
## render_report(config_filepath = "your/working/directory/summary_config.yaml",
##  output_file = "MutSeqR_Summary_Report.html",
##  output_format = "html_document")