SMAPObservations            package:SMAP            R Documentation

_C_o_n_s_t_r_u_c_t_o_r _f_o_r "_S_M_A_P_O_b_s_e_r_v_a_t_i_o_n_s" _o_b_j_e_c_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     A constructor for 'SMAPObservations-class' objects.

_U_s_a_g_e:

     SMAPObservations(value, chromosome, startPosition, endPosition,
                      name=character(0),
                      reporterId=as.character(1:length(value)))

_A_r_g_u_m_e_n_t_s:

   value: A vector of microarray intensity ratios (numeric).

chromosome: A vector of chromosome annotations (character).

startPosition: A vector of start positions (numeric).

endPosition: A vector of end positions (numeric).

    name: The name of the observation set (character).

reporterId: A vector of observation identifiers, e.g., probe ids
          (character).

_D_e_t_a_i_l_s:

     The vectors 'value', 'chromosome', 'startPosition', 'endPosition',
     and 'reporterId' must be of equal length.

_V_a_l_u_e:

     An object of class 'SMAPObservations-class'.

_A_u_t_h_o_r(_s):

     Robin Andersson, robin.andersson@lcb.uu.se

_R_e_f_e_r_e_n_c_e_s:

     Andersson, R., Bruder, C. E. G., Piotrowski, A., Menzel, U., Nord,
     H., Sandgren, J., Hvidsten, T. R., Diaz de Stahl, T., Dumanski, J.
     P., Komorowski, J., A Segmental Maximum A Posteriori Approach to
     Array-CGH Copy Number Profiling, submitted

_S_e_e _A_l_s_o:

     'smap', 'SMAPObservations-class', 'SMAPHMM-class'

_E_x_a_m_p_l_e_s:

     ## Load Glioblastoma multiforme data
     data(GBM)
     observations <- SMAPObservations(value=as.numeric(GBM[,2]),
                                      chromosome=as.character(GBM[,3]),
                                      startPosition=as.numeric(GBM[,4]),
                                      endPosition=as.numeric(GBM[,5]),
                                      name="G24460",
                                      reporterId=as.character(GBM[,1]))
     ## plot observations
     plot(observations, ylim=c(0,2))
     ## plot subset of observations (chromosome 9)
     ids <- which(chromosome(observations) == "9")
     plot(observations[ids])

