RangesList-methods        package:rtracklayer        R Documentation

_R_a_n_g_e_s _o_n _a _G_e_n_o_m_e

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

     Genomic coordinates are often specified in terms of a genome
     identifier, chromosome name, start position and end position. This
     information can be represented by a 'RangesList' instance, and the
     'rtracklayer' package adds convenience methods to 'RangesList' for
     the manipulation of genomic ranges. The spaces (or names) of
     'RangesList' are the chromosome names. The 'universe' slot
     indicates the genome, usually as given by UCSC (e.g. hg18).

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

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


      'chrom(x)': Gets the chromosome names (a factor) over the ranges
          in 'x'.

      'genome(x)', 'genome(x) <- value': Gets or sets the genome (a
          single string or 'NULL') for the ranges in 'x'; simple
          wrappers around 'universe' and 'universe<-', respectively.


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


      'GenomicRanges(start, end, chrom = NULL, genome = NULL)':
          Constructs a 'RangesList' containing ranges specified by
          'start' and 'end', optionally split into elements based on
          'chrom', a vector of chromosome identifiers (or 'NULL' for no
          splitting). The 'genome' argument should be a scalar string
          and is treated as the 'RangesList' universe. See the
          examples.


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

     Michael Lawrence

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

     GenomicRanges(c(1,2,3), c(5,2,8))
     GenomicRanges(c(1,2,3), c(5,2,8), c("chr1", "chr1", "chr2"))
     GenomicRanges(c(1,2,3), c(5,2,8), genome = "hg18")

