genomeSegment-class       package:rtracklayer       R Documentation

_C_l_a_s_s "_g_e_n_o_m_e_S_e_g_m_e_n_t"

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

     An object representing a segment of a genome.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects are normally created by a call of the following form:
     'genomeSegment(genome, chrom, start, end, segment)'. All
     parameters are optional and correspond to slots of the new
     'genomeSegment' instance, except for the 'segment' parameter,
     which serves as the base for the new instance. The slots of the
     new segment match those of 'segment', unless the call specifies
     other parameters, which override the corresponding slots in
     'segment'.

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


     '_g_e_n_o_m_e': Object of class '"character"' giving the name of the
          genome (e.g. "hg18"). 

     '_c_h_r_o_m': Object of class '"character"' giving the chromosome name
          (e.g. "chr22"). 

     '_s_t_a_r_t': Object of class '"numeric"' indicating the start position
          of the segment on the chromosome.

     '_e_n_d': Object of class '"numeric"' indicating the stop position of
          the segment on the chromosome. 

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


     '_m_e_r_g_e(_x, _y)' Merges two instances. The result has the same slot
          values as 'x', except the non-empty slots in 'y' override
          those from 'x'.

     '_g_e_n_o_m_e(_o_b_j_e_c_t)' Gets the genome identifier.

     '_g_e_n_o_m_e(_o_b_j_e_c_t) <- _v_a_l_u_e' Sets the genome identifier.

     '_c_h_r_o_m(_o_b_j_e_c_t)' Gets the 'chrom'osome identifier.

     '_c_h_r_o_m(_o_b_j_e_c_t) <- _v_a_l_u_e' Sets the 'chrom'osome identifier.

     '_s_t_a_r_t(_o_b_j_e_c_t)' Gets the start position.

     '_s_t_a_r_t(_o_b_j_e_c_t) <- _v_a_l_u_e' Sets the start position.

     '_e_n_d(_o_b_j_e_c_t)' Gets the end position.

     '_e_n_d(_o_b_j_e_c_t) <- _v_a_l_u_e' Sets the end position.

     '_o_b_j_e_c_t / _x' Zoom out 'x' times (expand segment by 'x/2' on each
          side).

     '_o_b_j_e_c_t * _x' Zoom in 'x' times (contract segment by 'x/2' on each
          side).


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

     Michael Lawrence

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

     'genomeSegment' for obtaining instances of this class.

