Transcript-class        package:GenomeGraphs        R Documentation

_R_e_p_r_e_s_e_n_t _k_n_o_w_n _t_r_a_n_s_c_r_i_p_t _i_s_o_f_o_r_m_s _a_s _a_n_n_o_t_e_d _b_y _E_n_s_e_m_b_l

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

     Represent known transcript isoforms as annoted by Ensembl

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

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


     '_i_d': Object of class '"character"', represents the gene
          identifier that should be used to retrieve the tanscript
          level annotation 

     '_t_y_p_e': Object of class '"character"', represents the type of
          identifiers used to specify the gene e.g. hgnc_symbol,
          entrezgene and ensembl_gene_id

     '_s_i_z_e': Object of class '"numeric"', represents the size of the
          plot of this object

     '_t_r_a_n_s_c_r_i_p_t_S_i_z_e': Object of class '"numeric"', represents the size
          of the transcripts in the plot

     '_n_u_m_O_f_T_r_a_n_s_c_r_i_p_t_s': Object of class '"numeric"', should not be
          used bu users 

     '_c_o_l_o_r': Object of class '"character"', color of the exons

     '_b_i_o_m_a_r_t': Object of class '"Mart"', containing the links to the
          Ensembl database.  This object should be created with the
          useMart function of the biomaRt package 

     '_e_n_s': Object of class '"data.frame"', should not be used by the
          users.  Contains the output from the biomaRt query 

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


     _d_r_a_w_G_D 'signature(.Object = "Transcript")': ...     

     _i_n_i_t_i_a_l_i_z_e 'signature(.Object = "Transcript")': ... 

     _s_h_o_w 'signature(object = "Transcript")': ... 

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

     Steffen Durinck

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

     http://www.stat.berkeley.edu/~steffen/

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

     objects to See Also as 'gdPlot'

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

     if(interactive()){
     data("unrData", package="GenomeGraphs")
     mart = useMart("ensembl", dataset="hsapiens_gene_ensembl")
     transcript = new("Transcript", id ="ENSG00000009307" , biomart = mart)
     gdPlot(list(transcript), minBase = min(exon@probeStart), maxBase=max(exon@probeEnd))
     }

