coverage               package:IRanges               R Documentation

_C_o_v_e_r_a_g_e _a_c_r_o_s_s _a _s_e_t _o_f _r_a_n_g_e_s

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

     Counts the number of times a position is represented in a set of
     ranges.

_U_s_a_g_e:

       coverage(x, start=NA, end=NA, ...)
       ## S4 method for signature 'IRanges':
       coverage(x, start=NA, end=NA, weight=1L)

_A_r_g_u_m_e_n_t_s:

       x: An IRanges or MaskCollection object. 

   start: A single integer specifying the position in 'x' where to
          start the extraction of the coverage. 

     end: A single integer specifying the position in 'x' where to end
          the extraction of the coverage. 

  weight: An integer vector specifying how much each element in 'x'
          counts. 

     ...: Further arguments to be passed to or from other methods. 

_V_a_l_u_e:

     An XRleInteger object representing the coverage of 'x' in the
     interval specified by the 'start' and 'end' arguments. An integer
     value called the "coverage" can be associated to each position in
     'x', indicating how many times this position is covered by the
     ranges stored in 'x'. Note that the positions in the returned
     XInteger object are to be interpreted as relative to the interval
     specified by the 'start' and 'end' arguments.

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

     XRleInteger-class, IRanges-class, MaskCollection-class

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

       x <- IRanges(start=c(-2L, 6L, 9L, -4L, 1L, 0L, -6L, 10L),
                    width=c( 5L, 0L, 6L,  1L, 4L, 3L,  2L,  3L))
       coverage(x, start=-6, end=20)  # 'start' and 'end' must be specified for
                                      # an IRanges object.
       coverage(shift(x, 2), start=-6, end=20)
       coverage(restrict(x, 1, 10), start=-6, end=20)
       coverage(reduce(x), start=-6, end=20)
       coverage(gaps(x, start=-6, end=20), start=-6, end=20)

       mask1 <- Mask(mask.width=29, start=c(11, 25, 28), width=c(5, 2, 2))
       mask2 <- Mask(mask.width=29, start=c(3, 10, 27), width=c(5, 8, 1))
       mask3 <- Mask(mask.width=29, start=c(7, 12), width=c(2, 4))
       mymasks <- append(append(mask1, mask2), mask3)
       coverage(mymasks)

