If you wish to disable a particular Flycheck just for this one file, you can also use a file-local variable definition.
You can do this interactively while in the file's buffer by typing
M-x add-file-local-variable flycheck-disabled-checkers RET
(emacs-lisp-checkdoc)
which will add a local variables section to the end of the file.
;; Local Variables:
;; flycheck-disabled-checkers: (emacs-lisp-checkdoc)
;; End:
This is like customizing flycheck-disabled-checkers
but only for the file.
This can also be customized on the level of the directory. http://www.gnu.org/software/emacs/manual/html_mono/emacs.html#Directory-Variables