Genome_intervals_stranded-classpackage:genomeIntervalsR Documentation

_C_l_a_s_s "_G_e_n_o_m_e__i_n_t_e_r_v_a_l_s__s_t_r_a_n_d_e_d"

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

     A set of genomic intervals with a specified strand.

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


     '._D_a_t_a': See 'Genome_intervals '

     '_a_n_n_o_t_a_t_i_o_n': A 'data.frame' (see 'Genome_intervals' for basic
          requirements). The 'annotation' moreover has a 'strand'
          column that is a factor with exactly two levels(typically
          '"+"' and '"-"'). 

     '_c_l_o_s_e_d': See 'Genome_intervals ' 

     '_t_y_p_e': See 'Genome_intervals ' 

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

     Class '"Genome_intervals"', directly. Class '"Intervals_full"', by
     class "Genome_intervals", distance 2. Class '"Intervals_virtual"',
     by class "Genome_intervals", distance 3. Class '"matrix"', by
     class "Genome_intervals", distance 4. Class '"array"', by class
     "Genome_intervals", distance 5. Class '"structure"', by class
     "Genome_intervals", distance 6. Class '"vector"', by class
     "Genome_intervals", distance 7, with explicit coerce.

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


     _c_o_e_r_c_e 'signature(from = "Genome_intervals_stranded", to =
          "character")': ... 

     _d_i_s_t_a_n_c_e__t_o__n_e_a_r_e_s_t 'signature(from = "Genome_intervals_stranded",
          to = "Genome_intervals_stranded")': ... 

     _i_n_t_e_r_v_a_l__c_o_m_p_l_e_m_e_n_t 'signature(x = "Genome_intervals_stranded")':
          ... 

     _i_n_t_e_r_v_a_l__i_n_t_e_r_s_e_c_t_i_o_n 'signature(x =
          "Genome_intervals_stranded")': ... 

     _i_n_t_e_r_v_a_l__o_v_e_r_l_a_p 'signature(to = "Genome_intervals_stranded", from
          = "Genome_intervals_stranded")': ... 

     _i_n_t_e_r_v_a_l__u_n_i_o_n 'signature(x = "Genome_intervals_stranded")': ... 

     _s_t_r_a_n_d 'signature(x = "Genome_intervals_stranded")': ... 

     _s_t_r_a_n_d<- 'signature(x = "Genome_intervals_stranded")': ... 

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

     'Genome_intervals' the parent class without strand.

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

     # The "Genome_intervals_stranded" class
     j <- new(
              "Genome_intervals_stranded",
              matrix(
                     c(1,2,  
                       3,5,
                       4,6,
                       8,9
                       ),
                     byrow = TRUE,
                     ncol = 2
              ),
              closed = matrix(
                                     c(
                                             FALSE, FALSE,
                                             TRUE, FALSE,
                                             TRUE, TRUE,
                                             TRUE, FALSE
                                      ),
                                     byrow = TRUE,
                             ncol = 2
                             ),
          annotation = data.frame(
                                     seq_name = factor( c("chr01","chr01", "chr02","chr02") ),
                                             strand = factor( c("+", "+", "+", "-") ),
                                             inter_base = c(FALSE,FALSE,FALSE,TRUE)
                                             )
              )

     ## print
     print(j)

     ## size of each interval as count of included bases 
     size(j)

     ## close intervals left and right (canonical representation)
     close_intervals(j)

