cdfAddPlasqTypes         package:affxparser         R Documentation

_A_d_d_s _t_h_e _P_L_A_S_Q _t_y_p_e_s _f_o_r _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 PLASQ types for the probes in a CDF structure.

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

_U_s_a_g_e:

     cdfAddPlasqTypes(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 'expos'. 

     ...: Not used.

_D_e_t_a_i_l_s:

     This function 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 PLASQ [1], and adds an integer [0,15]
     interepreted as one of 16 probe types.  In PLASQ these probe types
     are referred to as: 0=MMoBR, 1=MMoBF, 2=MMcBR, 3=MMcBF, 4=MMoAR,
     5=MMoAF, 6=MMcAR, 7=MMcAF, 8=PMoBR, 9=PMoBF, 10=PMcBR, 11=PMcBF,
     12=PMoAR, 13=PMoAF, 14=PMcAR, 15=PMcAF.

     Pseudo rule for finding out the probe-type value:

        *  PM/MM: For MMs add 0, for PMs add 8.

        *  A/B: For Bs add 0, for As add 4.

        *  o/c: For shifted (o) add 0, for centered (c) add 2.

        *  R/F: For antisense (R) add 0, for sense (F) add 1.

     Example: (PM,A,c,R) = 8 + 4 + 2 + 0 = 14 (=PMcAR)

_V_a_l_u_e:

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

plasqType: A 'vector' of 'integer's in [0,15].

_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.

