You have a JavaScript function and you want to execute it from ASP.NET code behind file. You can achieve this by using RegisterStartupScript method of ClientScript class as shown below:
Let's suppose you have following JavaScript function in your code.
<script type="text/javascript">
function SayMeHello()
{
alert('Hello');
}
</script>
In order to call it from code behind, use the following code
if (!ClientScript.IsStartupScriptRegistered("helloAlert"))
{
Page.ClientScript.RegisterStartupScript( this.GetType(), "helloAlert", "SayMeHello();", true);
}