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)           

