Gene-class           package:GenomeGraphs           R Documentation

_C_l_a_s_s "_G_e_n_e" _r_e_p_r_e_s_e_n_t_s _t_h_e _E_n_s_e_m_b_l _G_e_n_e _l_e_v_e_l _a_n_n_o_t_a_t_i_o_n

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

     Class "Gene" represents the Ensembl Gene level annotation.  Upon
     creation of an object of this class, intron and exon boundaries
     are retrieved from 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("Gene", ...)'.

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


     '_i_d': Object of class '"character"', representing a unique
          identifier for the gene or a vector of identifiers for genes
          that are located near each other (or at least on the same
          chromosome)

     '_t_y_p_e': Object of class '"character"', representing the type of
          identifier used, e.g. hgnc_symbol, entrezgene and
          ensembl_gene_id, check the listFilters function of the
          biomaRt package for more identifier options

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

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

     '_b_i_o_m_a_r_t': Object of class '"Mart"', contains the link to the
          Ensembl database and should be created using the useMart
          function from the biomaRt package 

     '_e_n_s': Object of class '"data.frame"', contains the output from
          the Ensembl query, users don't need to give a value to this 

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


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

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

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

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

     Jim Bullard and 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()){
     mart = useMart("ensembl", dataset="hsapiens_gene_ensembl")
     gene = new("Gene", id = "ENSG00000095203", type="ensembl_gene_id", biomart = mart)
     gdPlot(list(gene), minBase= 110974000, maxBase = 111122900)
     }

