1. How and where to include JavaScript Files in Angular Project?
You need to include your JS file in the asset folder and refer this JS file in .angular-cli.json file.
Refer the snapshot’s,
Folder structure should be like this.

.angular-cli.json

2. How to call the JavaScript Functions from Typescript class?
your TS should be like this.

myJsFile.js file content.

This sample logic mentioned above will work, I have tried and tested using version 4, So I am expecting it to work with version 5 also.
Updating the answer for the new Angular version release. Working
perfectly till version11.2.6.
Find the code (function with parameter) here for Angular11