cdfAddBaseMmCounts        package:affxparser        R Documentation

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

     Adds the number of allele A and allele B mismatching nucleotides
     of the probes in a CDF structure.

     This 'function' is design to be used with 'applyCdfGroups'() on an
     Affymetrix Mapping (SNP) CDF 'list' structure.

     Identifies the number of nucleotides (bases) in probe sequences
     that mismatch the the target sequence for allele A and the allele
     B, as used by [1].

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

     cdfAddBaseMmCounts(groups, ...)

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

  groups: A 'list' structure with groups. Each group must contain the
          fields 'tbase', 'pbase', and 'offset' (from
          'cdfAddProbeOffsets'()). 

     ...: Not used.

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

     Note that the above counts can be inferred from the CDF structure
     alone, i.e. no sequence information is required. Consider a probe
     group interrogating allele A.  First, all PM probes matches the
     allele A target sequence perfectly regardless of shift. Moreover,
     all these PM probes mismatch the allele B target sequence at
     exactly one position.  Second, all MM probes mismatches the allele
     A sequence at exactly one position.  This is also true for the
     allele B sequence, _except_ for an MM probe with zero offset,
     which only mismatch at one (the middle) position. For a probe
     group interrogating allele B, the same rules applies with labels A
     and B swapped. In summary, the mismatch counts for PM probes can
     take values 0 and 1, and for MM probes they can take values 0, 1,
     and 2.

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

     Returns a 'list' structure with the same number of groups as the
     'groups' argument.  To each group, two fields is added:

mmACount: The number of nucleotides in the probe sequence that
          mismatches the target sequence of allele A.

mmBCount: The number of nucleotides in the probe sequence that
          mismatches the target sequence of allele B.


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

     Henrik Bengtsson (<URL: http://www.braju.com/R/>)

_R_e_f_e_r_e_n_c_e_s:

     [1] LaFramboise T, Weir BA, Zhao X, Beroukhim R, Li C, Harrington
     D, Sellers WR, and Meyerson M. _Allele-specific amplification in
     cancer revealed by SNP array analysis_, PLoS Computational
     Biology, Nov 2005, Volume 1, Issue 6, e65.
      [2] Affymetrix, _Understanding Genotyping Probe Set Structure_,
     2005. <URL:
     http://www.affymetrix.com/support/developer/whitepapers/genotyping_probe_set_structure.affx>

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

     To add required probe offsets, 'cdfAddProbeOffsets'().
     'applyCdfGroups'().

