Check this blog by Steve Peschka. I have set up provider hosted app in SiteMinder protected SharePoint 2013 using that blog. To impersonate a user you need to create a ClaimsIdentity of the user and insert it to the HttpContext as current user. Sample code for that below:
var identity = new ClaimsIdentity(AuthenticationTypes.Federation, "http://schemas.xmlsoap.org/claims/useridentifier", String.Empty);
identity.AddClaim(new Claim("http://schemas.xmlsoap.org/claims/useridentifier", userId, "http://www.w3.org/2001/XMLSchema#string"));
identity.AddClaim(new Claim(ClaimTypes.Email, smtp, "http://www.w3.org/2001/XMLSchema#string"));
identity.AddClaim(new Claim("http://schemas.xmlsoap.org/ws/2005/05/identity/claims/sip", nameIdentifier, "http://www.w3.org/2001/XMLSchema#string"));
ClaimsPrincipal principal = new ClaimsPrincipal(identity);
Set this ClaimsPrincipalas the Httpcontext user.
The claim values to be passed are smtp= email of user , nameidentifier=loginname of user , userId= Account name of user