Perpendicular distance from chord to circle

The perpendicular distance, if I understand this correctly, is just the distance from the point to the circle, along the radius. So given a cord, and a point on it, you can calculate the $x$ and $y$ positions of the point in terms of the distance from one end. Then the distance between that point and the circle is just $R-\sqrt{x^2+y^2}$. You would need to give more information about how you define the cord, in order to get a better answer.

Let a unit circle

$$x^2+y^2=1$$

and a horizontal chord

$$y=h.$$

The vertical distance is given by

$$y-h=\sqrt{1-x^2}-h,$$ for $x$ in $\left[-\sqrt{1-h^2},\sqrt{1-h^2}\right].$