It is still only a few information that you provide. Not easy to help.
If you are using flexdashboard, it is possible that you produced HTML file (either self contained one so a single HTML, or a folder with HTML and its resources). So you want probably to publish in sharepoint the HTML results and not the Rmd file right ? Your question is not clear about that.
For HTML, you should contact any admin of your sharepoint server so know how to create a sharepoint website or networkf drive where you can serve HTML files. If this sharepoint destination is accessible with URL in browser, and you put your files there provided that you sharepoint admin allows that, then it should be enough to share the output.
This is not specific to R Markdown, it is more generic : How can you serve a static website in your sharepoint ?