arrayTrend               package:MANOR               R Documentation

_S_p_a_t_i_a_l _t_r_e_n_d _o_f _m_i_c_r_o_a_r_r_a_y _s_p_o_t_s _s_t_a_t_i_s_t_i_c

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

     The function 'arrayTrend' computes the spatial trend.

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

     arrayTrend.default(Statistic, Col, Row, ...)
     arrayTrend.arrayCGH(arrayCGH, variable, ...)

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

Statistic: Statistic to be smoothed.

     Col: Vector of columns coordinates.

     Row: Vector of rows coordinates.

arrayCGH: Object of class 'arrayCGH'.

variable: Variable to be smooth.

     ...: Parameters to be passed to 'loess' function.

_D_e_t_a_i_l_s:

     Spatial trend of microarray spots statistic.

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

     Either a data frame with elements : 

   Trend: 

     Col: 

     Row: 


     or the element 'Trend' is added to the data.frame 'arrayValues' of
     the 'arrayCGH' object.

_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, Philippe.Hupe@curie.fr.

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

     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.

_S_e_e _A_l_s_o:

     'loess', 'loess.control'.

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

     data(spatial)  ## arrays with local spatial effects

     edgeTrend <- arrayTrend(edge, "LogRatio", span=0.03, degree=1,
     iterations=3, family="symmetric") 
     arrayPlot(edgeTrend, "Trend", main="Spatial trend of array CGH", bar="v") 

