Tailoring the properties of graphene has been the subject of very intensive research during the past few years. Such modification can be readily achieved using chemical functionalization with foreign atoms thanks to the two-dimensional nature of the material. The exact impact of such chemical treatment cannot always be accurately tackled experimentally, thus requiring active input from modeling and numerical simulations. Theoretical models predict weak localization to occur in graphene under certain specific conditions, including the mixing between inequivalent K-point valleys induced by short-range disorder. Mesoscopic computer simulations based on accurate parameters extracted from first-principles Density Functional Theory calculations, and applied to realistic graphene samples (with sizes comparable to experimental ones), allow to verify the existence of such quantum interference effects, in both hydrogenated and ozonated graphene. The seminal work by Geim and Novoselov suggested an Anomalous Quantum Hall Effect in graphene. In order to observe the very characteristic quantization of states in transverse conductivity measurements, the disordered system should combine the presence of both localized and extended states at specific critical energies, separated by mobility edges. The specific impact of disorder on this new quantum Hall effect is still a strongly debated issue among the theoretical community, due to the complexity of the calculations that have to be performed on realistic graphene samples. The present work extends the knowledge on simplified disorder models to the realistic cases of oxygen functionalization and hydrogenation on the transport properties of graphene. Particular attention is given to the specific impact of symmetry breaking induced by the non-equivalence of the two sub-lattices inherently present in the hexagonal structure. By including the effect of an external perpendicular magnetic field, the impact of symmetry preserving disorder on the Hall quantization is partially clarified. The appearance of previously unknown critical states specifically due to disorder in the diagonal conductivity is confirmed using a new formalism, which allows to predict the Hall conductivity. In order to extend the range of possible applications of graphene-based material, the spin degree of freedom has to be considered in addition to the conventional charge component of the carriers. In this context, a better understanding of possible intrinsic magnetism in graphene is required. Presently, no full consensus exists in the community regarding the possibility to induce paramagnetic centers and/or long-range interaction coupling between these local magnetic moments. A theoretical model is proposed allowing to check the existence of (anti)-ferromagnetism in graphene induced by hydrogen functionalization, through the observation of possible magneto-resistivity fingerprints.