RangesList-utils           package:IRanges           R Documentation

_R_a_n_g_e_s_L_i_s_t _u_t_i_l_i_t_y _f_u_n_c_t_i_o_n_s

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

     Utility functions for manipulating 'RangesList' objects.

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

     ## S4 method for signature 'RangesList':
     gaps(x, start=NA, end=NA)
     ## S4 method for signature 'RangesList':
     reduce(x, with.inframe.attrib = FALSE)

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

       x: A 'RangesList'

   start: The start of the range over which to calculate the gaps. If
          'NA', use the minimum start position in the 'Ranges'
          instance.

     end: The end of the range over which to calculate the gaps. If
          'NA', use the maximum end position in the 'Ranges' instance.

with.inframe.attrib: Ignored.

_D_e_t_a_i_l_s:

     The 'gaps' function takes the complement (the 'gaps') of each
     element in the list and returns the result as a 'RangesList'.

     The 'reduce' method merges (via 'reduce') all of the elements into
     a single 'Ranges' instance and returns the result as a length-one
     'RangesList'.

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

     A 'RangesList' instance. For 'gaps', length is the same as that of
     'x'. For 'reduce', length is one.

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

     Michael Lawrence, H. Pages

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

     'RangesList', 'reduce', 'gaps'

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

       # 'gaps'
       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))
       collection <- RangesList(one = range1, range2)

       # these two are the same
       RangesList(gaps(range1), gaps(range2))
       gaps(collection)

       # 'reduce'
       range2 <- IRanges(start=c(45,20,1), end=c(100,80,5))
       collection <- RangesList(one = range1, range2)

       # and these two are the same
       reduce(collection)
       RangesList(asNormalIRanges(IRanges(c(1,20), c(8, 100)), force=FALSE))

