nem              package:MANOR              R Documentation(latin1)

_S_p_a_t_i_a_l _C_l_a_s_s_i_f_i_c_a_t_i_o_n _b_y _E_M _a_l_g_o_r_i_t_h_m

_D_e_s_c_r_i_p_t_i_o_n:

     The function 'nem' computes spatial classification by EM
     algorithm.

_U_s_a_g_e:

     ## Default S3 method:
     nem(LogRatio, Col, Row, nk=nk, beta=1, iters=2000, ...)
     ## S3 method for class 'arrayCGH':
     nem(arrayCGH, variable, nk=5, beta=1, iters=2000, ...)

_A_r_g_u_m_e_n_t_s:

LogRatio: Vector that corresponds to the values to be classified.

     Col: Vector of columns coordinates.

     Row: Vector of rows coordinates.

      nk: Integer value corresponding to the number classes.

    beta: Scale parameter for importance of spatial information. 

   iters: Maximum number of iterations allowed.

arrayCGH: Object of class 'arrayCGH'.

variable: Variable that corresponds to the values to be classified.

     ...: ...

_V_a_l_u_e:

     Either a data frame with the following added elements: 

 ZoneNem: Vector of label zones.

 ZoneNem: Vector of label zones.

_N_o_t_e:

     People interested in tools for array-CGH analysis can visit our
     web-page: <URL: http://bioinfo.curie.fr>.

_A_u_t_h_o_r(_s):

     Philippe Hup, manor@curie.fr.

_R_e_f_e_r_e_n_c_e_s:

  C. Ambroise, _Approche probabiliste en classification automatique et
     contraintes de voisinage_, Ph.D. thesis, Universit de Technologie
     de Compigne, 1996.

  C. Ambroise, M. Dang, and G. Govaert, _Clustering of spatial data by
     the em algorithm_ in Geostatistics for Environmental Applications,
     A. Soares, J. Gomez-Hernandez, and R. Froidevaux, Eds., pp.
     493-504. Kluwer Academic Publisher, 1997.

  P. Neuvial, P. Hup, I. Brito, S. Liva, E. Mani, C. Brennetot, A.
     Aurias, F. Radvanyi, and E. Barillot. _Spatial normalization of
     array-CGH data_. In preparation. 

_E_x_a_m_p_l_e_s:

     data(spatial)  ## arrays with local spatial effects

     ## Plot of LogRatio measured on the array CGH
     ## Not run: 
     arrayPlot(edge,"LogRatio", main="Log2-Ratio measured on the array
     CGH", zlim=c(-1,1), bar="v", mediancenter=TRUE) 
     ## End(Not run)

     ## Spatial trend of the scaled log-ratios (the variable "ScaledLogRatio"
     ## equals to the log-ratio minus the median value of the corresponding chromosome arm) 
     edgeTrend <- arrayTrend(edge, variable="ScaledLogRatio",
     span=0.03, degree=1, iterations=3, family="symmetric")

     ## Not run: 
     arrayPlot(edgeTrend, variable="Trend", main="Spatial trend of the array CGH", bar="v") 
     ## End(Not run)

     ## Classification with spatial constraint of the spatial trend
     edgeNem <- nem(edgeTrend, variable="Trend")
     ## Not run: 
     arrayPlot(edgeNem, variable="ZoneNem", main="Spatial zones identified by nem", bar="v")
     ## End(Not run)

