probeAnno-class            package:Ringo            R Documentation

_C_l_a_s_s "_p_r_o_b_e_A_n_n_o"

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

     A class that holds the mapping between reporters/probes on a
     microarray and their genomic match  position(s) in a chosen
     genome.

_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("probeAnno", map,
     arrayName, genome)'.

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


     '_m_a_p': Object of class '"environment"' This map consists of four
          vectors for each chromosome/strand, namely, say for
          chromosome 1:

          _1._s_t_a_r_t genomic start coordinates of probe matches on
               chromosome 1

          _1._e_n_d genomic start coordinates of probe matches on
               chromosome 1

          _1._i_n_d_e_x identifier of probes matching at these coordinates

          _1._u_n_i_q_u_e vector of the same length as the three before;
               encoding how many matches the corresponding probe has in
               the given file or 'data.frame'. An entry of '0'
               indicates that the probe matching at this position has
               only this one match.

     '_a_r_r_a_y_N_a_m_e': Object of class '"character"', the name or identifier
          of the microarray design, e.g.
          '2005-06-17_Ren_MM5Tiling_Set1'

     '_g_e_n_o_m_e': Object of class '"character"', which genome the
          reporters have been mapped to

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


     _a_r_r_a_y_N_a_m_e obtain the microarray platform name

     _a_r_r_a_y_N_a_m_e<- replace the microarray platform name

     [ get elements from the 'map' environment

     [<- assign elements to the 'map' environment

     _c_h_r_o_m_o_s_o_m_e_N_a_m_e_s obtain a character vector holding the names of the
          chromosomes for which the probeAnno objects holds a mapping.

     _g_e_t get elements from the 'map' environment

     _i_n_i_t_i_a_l_i_z_e create mew probeAnno object

     _l_s list elements of the 'map' environment 

     _g_e_n_o_m_e obtain the description of the genome the reporters were
          mapped to

     _g_e_n_o_m_e<- replace the description of the genome the reporters were
          mapped to

     _a_s signature(from="environment"); function to coerce old-style
          'probeAnno' environments to new-style 'probeAnno' objects.
          Simply creates a new object with the old environment in its
          'map' slot

_N_o_t_e:

     'probeAnno' objects used to be environments and are still in
     package 'tilingArray'

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

     Joern Toedling toedling@ebi.ac.uk; Wolfgang Huber

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

     posToProbeAnno

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

       pa <- new("probeAnno")
       pa["X.start"] <- seq(5000,10000,by=1000)
       if (interactive()) show(pa)
       pa2 <- posToProbeAnno(file.path(system.file("exData",package="Ringo"),
                                       "MOD_2003-12-05_SUZ12_1in2.pos"))
       arrayName(pa2) <- "NimbleGen MOD_2003-12-05_SUZ12_1in2"
       genome(pa2) <- "H. sapiens (hg18)"
       show(pa2)
       head(pa2["9.start"])

