RangesList-class           package:IRanges           R Documentation

_L_i_s_t _o_f _R_a_n_g_e_s

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

     An extension of 'TypedList' that holds only 'Ranges' instances.
     Useful for storing ranges over a set of spaces (e.g. chromosomes),
     each of which requires a separate 'Ranges' instance.

_A_c_c_e_s_s_o_r_s:

     In the code snippets below, 'x' is a 'RangesList' object. All
     accessors collapse over the spaces.


      'start(x)': Get the starts of the ranges.

      'end(x)': Get the ends of the ranges.

      'width(x)': Get the widths of the ranges.

      'isEmpty(x)': Gets a logical vector indicating which elements are
          empty (length zero).

_C_o_n_s_t_r_u_c_t_o_r:


      'RangesList(...)': Each 'Ranges' in '...' becomes an element in
          the new 'RangesList', in the same order. This is analogous to
          the 'list' constructor, except every argument in '...' must
          be derived from 'Ranges'. 


_C_o_e_r_c_i_o_n:

     In the code snippets below, 'x' is a 'RangesList' object.


      'as.data.frame(x, row.names = NULL, optional = FALSE)': Coerces
          'x' to a 'data.frame'. Essentially the same as calling
          'as.data.frame(unlist(x))'.

      'as(from, "IRangesList")': Coerces 'from', a 'RangesList', to an
          'IRangesList', requiring that all 'Ranges' elements are
          coerced to internal 'IRanges' elements. This is a convenient
          way to ensure that all 'Ranges' have been imported into R
          (and that there is no unwanted overhead when accessing them).


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

     Michael Lawrence

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

       range1 <- IRanges(start=c(1,2,3), end=c(5,2,8))
       range2 <- IRanges(start=c(15,45,20,1), end=c(15,100,80,5))
       named <- RangesList(one = range1, two = range2)
       length(named) # 2
       start(named) # same as start(c(range1, range2))
       names(named) # "one" and "two"
       named[[1]] # range1
       unnamed <- RangesList(range1, range2)
       names(unnamed) # NULL

       # same as list(range1, range2)
       as.list(RangesList(range1, range2))

       # coerce to data.frame
       as.data.frame(named)

