SpliceSitesGenomic-class     package:splicegear     R Documentation

_C_l_a_s_s "_S_p_l_i_c_e_S_i_t_e_s_G_e_n_o_m_i_c"

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

     A class to store alternative splicing information on a genomic
     point of view.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form
     'new("SpliceSitesGenomic", seq, seq.length, spsiteIpos,
     spsiteIIpos, spsiteIIIpos, spsiteIpos.pData, spsiteIIpos.pData,
     spsiteIIIpos.pData, ...)'.

_S_l_o_t_s:


     '_v_a_r_i_a_n_t_s': Object of class '"list"'. There is one element per
          splice variant. Each element in the list should be a vector
          of integers. Each integer refers to an exon. The sequence of
          integers determines the sequence of exons in the splice
          variant.

     '_s_e_q': Object of class '"character", from class "SpliceSites"'.

     '_s_e_q._l_e_n_g_t_h': Object of class '"integer", from class
          "SpliceSites"'.

     '_s_p_s_i_t_e_I_p_o_s': Object of class '"matrix", from class
          "SpliceSites"'.

     '_s_p_s_i_t_e_I_I_p_o_s': Object of class '"integer", from class
          "SpliceSites"'. This should not have any practical use in
          this class.

     '_s_p_s_i_t_e_I_I_I_p_o_s': Object of class '"matrix", from class
          "SpliceSites"'. This should not have any practical use in
          this class.

     '_s_p_s_i_t_e_I_p_o_s._p_D_a_t_a': Object of class '"AnnotatedDataFrame", from
          class "SpliceSites"'.

     '_s_p_s_i_t_e_I_I_p_o_s._p_D_a_t_a': Object of class '"AnnotatedDataFrame", from
          class "SpliceSites"'. This should not have any practical use
          in this class.

     '_s_p_s_i_t_e_I_I_I_p_o_s._p_D_a_t_a': Object of class '"AnnotatedDataFrame", from
          class "SpliceSites"'. This should not have any practical use
          in this class.

_E_x_t_e_n_d_s:

     Class '"SpliceSites"', directly.

_M_e_t_h_o_d_s:


     _p_l_o_t 'signature(x = "SpliceSitesGenomic", y = "missing")': a
          plotting method for demonstration purposes. 

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

     'SpliceSites-class' and 'plot.SpliceSitesGenomic'.

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

     ## a 10 bp window
     seq.length <- as.integer(10)
     ## positions of the exons
     spsiteIpos <- matrix(c(1, 3.5, 5, 9, 3, 4, 8, 10), nc=2)
     ## known variants
     variants <- list(a=c(1,2,3,4), b=c(1,2,3), c=c(1,3,4))

     spvar <- new("SpliceSitesGenomic", spsiteIpos=spsiteIpos,
              variants=variants, seq.length=seq.length)

     plot(spvar)

