Disagree with study by Yankee (4)
I believe the answer is:
deny
'disagree' is the definition.
(I know that deny is a more specific form of the action contradict)
'study by yankee' is the wordplay.
'study' becomes 'den' (term for a study or office).
'by' is a charade indicator (letters next to each other).
'yankee' becomes 'Y' (phonetic alphabet: alpha, bravo, charlie etc.).
'den'+'y'='DENY'
'with' acts as a link.
(Other definitions for deny that I've seen before include "Claim to be untrue" , "Declare not to be true" , "Refute, contradict" , "Refuse to accept" , "Refuse to admit (something)" .)