Below is an example of how to use PDFDoc.RunJS, A premium license is required for this method.

private async System.Threading.Tasks.Task testJsAsync()
        {
            StorageFolder localFolder = ApplicationData.Current.LocalFolder;
            StorageFile srcFile = await localFolder.GetFileAsync("Test.pdf");

            IRandomAccessStream stream = await srcFile.OpenAsync(FileAccessMode.ReadWrite);
            if(stream != null)
            {
                String js = "app.alert({cMsg:\"Hello World\", cTitle:\"Testing\", nIcon: 1, nType: 1});";
                applyJs(stream, js);

                //test set author and save PDF file.
                js = "console.println(\"Author before set:\" + this.author);this.author='radaee';console.println(\"Author after set:\" + this.author);";
                applyJs(stream, js);

                //test add and set annotation.
                js = "var sqannot = this.addAnnot({type: \"Square\", rect: [10, 10, 110, 110], page: 1, width: 10, strokeColor: [\"RGB\", 0, 0, 1]});console.println(\"fill color before set:\" + sqannot.fillColor);sqannot.fillColor=[\"RGB\", 1, 0, 0];console.println(\"fill color after set:\" + sqannot.fillColor);console.println(\"page no is:\" + sqannot.page);sqannot.page = 2;console.println(\"page set to:\" + sqannot.page);console.println(\"rect before set:\" + sqannot.rect);sqannot.rect=[50, 50, 150, 150];console.println(\"rect after set:\" + sqannot.rect);";
                applyJs(stream, js);

                //test bookmarks (assuming the pdf already contains bookmarks)
                js = "console.println(\"bookmark label:\" + this.bookmarkRoot.children[0].name);this.bookmarkRoot.children[0].name='123';console.println(\"after set:\" + this.bookmarkRoot.children[0].name);";
                applyJs(stream, js);

                //test Exception catch
                js = "try{app.alert();}catch(e){console.println(e);}";
                applyJs(stream, js);

                //test Uncaught Exception.
                js = "console.print('test');";
                applyJs(stream, js);
            }
        }

        private void applyJs(IRandomAccessStream stream, String js)
        {
            PDFDoc doc = new PDFDoc();
            if (doc.Open(stream, "") == PDF_ERROR.err_ok) //no password        
            {    
                try
                {
                    doc.RunJS(js, new JSDelegate());
                    doc.Save();
                }
                catch (Exception e)
                {
                    Debug.WriteLine("Exception: " + e.Message);
                }
                String val = doc.GetMeta("Author");
            }
            doc.Close();
        }

        class JSDelegate : PDFJSDelegate
        {
            public void OnConsole(int cmd, string para)
            {
                switch (cmd)
                {
                    case 0://clear
                        Debug.WriteLine("Clear");
                        break;
                    case 1://hide
                        Debug.WriteLine("Hide");
                        break;
                    case 2://println
                        {
                            Debug.WriteLine(para + "\r\n");
                        }
                        break;
                    case 3://show
                        Debug.WriteLine("Show");
                        break;
                }
            }

            public int OnAlert(int btn, string msg, string title)
            {
                Debug.WriteLine("Alert {title:\"" + title + "\",message:\"" + msg + "\",button:" + btn + ",return:1}\r\n");
                return 1;
            }

            public bool OnDocClose()
            {
                return true;
            }

            public string OnTmpFile()
            {
                return "";
            }

            public void OnUncaughtException(int code, string msg)
            {
                Debug.WriteLine(msg + "\r\n");
            }
        }