SpliceSites-class         package:splicegear         R Documentation

_C_l_a_s_s "_S_p_l_i_c_e_S_i_t_e_s"

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

     A class to store (putative) splice sites

_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("SpliceSites",
     ...)'.

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


     '_p_r_o_b_e_p_o_s': Object of class '"matrix"'. A two-columns matrix to
          store the begin and end positions of probes (one row per
          probe).

     '_s_e_q': Object of class '"character"'. The reference sequence.

     '_s_e_q._l_e_n_g_t_h': Object of class '"integer"'. The length for the
          reference sequence (used when the slot 'seq' is set to '""').

     '_s_p_s_i_t_e_I_p_o_s': Object of class '"matrix"'. A two-columns matrix to
          store the begin and end positions of type I splice variant.

     '_s_p_s_i_t_e_I_I_p_o_s': Object of class '"integer"'. A vector to store the
          positions for type II splice variants.

     '_s_p_s_i_t_e_I_I_I_p_o_s': Object of class '"matrix"'. Idem 'spsiteIpos', but
          for type III splice variants.

     '_s_p_s_i_t_e_I_p_o_s._p_D_a_t_a': Object of class '"AnnotatedDataFrame"'. Used
          to store covariate information related to the splice
          variants.

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

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

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


     _s_h_o_w 'signature(object = "SpliceSites")': A printing method. 

     _p_l_o_t 'signature(x = "SpliceSites", y = "missing")': A plotting
          method 

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

     laurent@cbs.dtu.dk

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

     "Plenty of splicin' or 'can regular Affymetrix chips be used to
     observe alternative splicing ?'", Gautier L. et al., 2003,
     manuscript in preparation (and the title might have to chang...).

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

     'isSpliceSiteOnProbe', 'isProbeOnSpliceSite', 'plot.SpliceSites',
     'spliceset'.

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

     data(spliceset)

     print(spliceset)

     par(mfrow=c(1,2))

     plot(spliceset, main=attr(spliceset, "name"))

     ## filter out supporting matches with unique positions
     filter.typeI <- function(x) {unique(x[duplicated(x), , drop=FALSE])}
     spliceset.filter <- spliceset
     sSites <- spliceset.filter@spliceSites
     sSites@spsiteIpos <- filter.typeI(sSites@spsiteIpos)
     spliceset.filter@spliceSites <- sSites
     ## plot the resulting new object
     plot(spliceset.filter)

