posToProbeAnno             package:Ringo             R Documentation

_F_u_n_c_t_i_o_n _f_o_r _c_r_e_a_t_i_n_g _a _p_r_o_b_e_A_n_n_o _e_n_v_i_r_o_n_m_e_n_t

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

     This function allows the user to create a probeAnno environment
     that holds the mapping between probes on the array and their
     genomic match position(s). As input, the function takes either a.)
     one of NimbleGen's POS file or a similar file that holds the
     mapping of probes to the genome. OR b.) a 'data.frame' holding
     this information

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

     posToProbeAnno(pos, chrNameColumn = "CHROMOSOME",
        probeColumn = "PROBE_ID", chrPositionColumn = "POSITION",
        lengthColumn = "LENGTH", sep="\t", genome="unknown",
        microarrayPlatform="unknown", verbose = TRUE, ...)

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

     pos: either a file-name that specifies the path to the POS or
          other mapping file OR a data.frame holding the mapping

chrNameColumn: name of the column in the file or 'data.frame' that
          holds the chromosome name of the match

probeColumn: name of the column that holds the matching probe's unique
          identifier

chrPositionColumn: name of the column that holds the match genomic
          position/coordinate on the chromosome

lengthColumn: name of the column that holds the length of the  match
          position, in case of perfect match should correspond to the
          sequence length of the probe

     sep: string; denotes the seperator between elements in the
          supplied mappings file 'pos'; passed on to function 'scan';
          ignored if 'pos' is not a filename.

  genome: string; denotes genome (and assembly) the reporters have been
          mapped to for this probeAnno object, e.g. "M. musculus (mm9)"

microarrayPlatform: string; denotes the commercial or custom microarray
          platform/design that holds the reporters whose mapping is
          stored in this probeAnno object, e.g. "NimbleGen MOD SUZ12"

 verbose: logical; should progress be written to STDOUT?

     ...: further arguments passed on to function 'scan', which is used
          for reading in the file 'pos'.

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

     The default column names correspond to the column names in a
     NimbleGen POS file.

     For custom mappings, using the tools Exonerate, BLAT or MUMmer,
     the scripts directory of this package holds Perl scripts to
     generate such a POS file from the respective output files.

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

     The results is an object of class 'probeAnno'.

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

     Joern Toedling toedling@ebi.ac.uk

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

     'probeAnno-class', 'scan'

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

      exPos <- read.delim(file.path(system.file("exData",package="Ringo"),
                          "MOD_2003-12-05_SUZ12_1in2.pos"),
                          header=TRUE,as.is=TRUE)
      str(exPos)
      exProbeAnno <- posToProbeAnno(exPos,
          genome="M. musculus (assembly mm8)",
          microarrayPlatform="NimbleGen 2005-06-17_Ren_MM5Tiling_Set1")
      ## is equivalent to 
      exProbeAnno2 <- posToProbeAnno(file.path(
         system.file("exData",package="Ringo"),"MOD_2003-12-05_SUZ12_1in2.pos"),
         genome="M. musculus (assembly mm8)",
         microarrayPlatform="NimbleGen 2005-06-17_Ren_MM5Tiling_Set1")
      ls(exProbeAnno)
      chromosomeNames(exProbeAnno2)

