cdfAddBaseMmCounts        package:affxparser        R Documentation

_A_d_d_s _t_h_e _n_u_m_b_e_r _o_f _a_l_l_e_l_e _A _a_n_d _a_l_l_e_l_e _B _m_i_s_m_a_t_c_h_i_n_g _n_u_c_l_e_o_t_i_d_e_s _o_f _t_h_e _p_r_o_b_e_s _i_n _a _C_D_F _s_t_r_u_c_t_u_r_e

_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.

     normal-bracket31bracket-normal

_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'().

