PMindex             package:tilingArray             R Documentation

_F_i_n_d _t_h_e _i_n_d_e_x _o_f _t_h_e _e_x_a_c_t _m_a_t_c_h (_P_M) _o_r _b_a_c_k_g_r_o_u_n_d _p_r_o_b_e_s _f_r_o_m _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:

     Find the index of the exact match (PM) or background probes from a
     probeAnno environment

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

     PMindex(probeAnno)
     BGindex(probeAnno)

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

probeAnno: environment with probe annotations. See package
          'davidTiling' for an example (?probeAnno).

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

     These functions extract the exact match probes (PM) or background
     probes (from intergenic regions outside of known annotations)
     indices from 'probeAnno'.   These indices can be used to select
     the relevant rows of intensity data from the 'ExpressionSet'
     object for plotting and normalization.

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

     Numeric vector of indices.

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

     Matt Ritchie <ritchie@ebi.ac.uk>

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

     ## library(davidTiling)
     ## data(davidTiling)
     ## data(probeAnno)
     ## pmind <- PMindex(probeAnno)
     ## mmind <- MMindex(probeAnno)
     ## bgind <- BGindex(probeAnno)
     ## boxplot(as.data.frame(log2(exprs(davidTiling))[pmind,]), outline=FALSE)           

