Set rootViewController of UINavigationController by method other than initWithRootViewController

You can solve this by calling setViewControllers.

Like this:

UINavigationController *navigationController = [[UINavigationController alloc] initWithNavigationBarClass:[MyNavigationBar class] toolbarClass:[UIToolbar class]];

[navigationController setViewControllers:@[yourRootViewController] animated:NO];

Swift version:

let navigationController = UINavigationController(navigationBarClass: MyNavigationBar.self, toolbarClass: UIToolbar.self)

navigationController.setViewControllers([yourRootViewController], animated: false)

Knowledge Sharing Using Swift:

Changing root view controller from class other than app delegate.swift

let appdelegate = UIApplication.sharedApplication().delegate as! AppDelegate
let mainStoryboard: UIStoryboard = UIStoryboard(name: "Main", bundle: nil)
var homeViewController = mainStoryboard.instantiateViewControllerWithIdentifier("HomeViewController") as! HomeViewController
let nav = UINavigationController(rootViewController: homeViewController)
appdelegate.window!.rootViewController = nav

Hope this will helpful for someone.

Edited:

Changing rootviewcontroller With Animation can be achieve with:

 UIView.transitionWithView(self.window!, duration: 0.5, options: UIViewAnimationOptions.TransitionFlipFromLeft, animations: {
    self.window?.rootViewController = anyViewController
}, completion: nil)

We can write generalise method too similar to this.

this one works for me, hope it helps you,

let rootVC:LoginViewController = self.storyboard?.instantiateViewControllerWithIdentifier("LoginViewController") as! LoginViewController
let nvc:UINavigationController = self.storyboard?.instantiateViewControllerWithIdentifier("RootNavigationController") as! UINavigationController
nvc.viewControllers = [rootVC]
UIApplication.sharedApplication().keyWindow?.rootViewController = nvc