mm                   package:oligo                   R Documentation

_A_c_c_e_s_s_o_r_s _a_n_d _r_e_p_l_a_c_e_m_e_n_t _m_e_t_h_o_d_s _f_o_r _t_h_e _P_M/_M_M/_B_G _m_a_t_r_i_c_e_s.

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

     Accessors and replacement methods for the PM/MM/BG matrices.

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

     mm(object, subset = NULL)
     pm(object, subset = NULL, ...)
     bg(object, subset = NULL)
     mm(object)<-value
     pm(object)<-value
     bg(object)<-value

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

  object: 'FeatureSet' object.

  subset: Not implemented yet.

   value: 'matrix' object.

     ...: Extra arguments for future implementation.

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

     For all objects but 'TilingFeatureSet2', these methods will return
     matrices. In case of 'TilingFeatureSet2' objects, the value is a
     3-dimensional array (probes x samples x channels).

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

     if (require(maqcExpression4plex) & require(pd.hg18.60mer.expr)){
     xysPath <- system.file("extdata", package="maqcExpression4plex")
     xysFiles <- list.xysfiles(xysPath, full.name=TRUE)
     ngsExpressionFeatureSet <- read.xysfiles(xysFiles)
     pm(ngsExpressionFeatureSet)[1:10,]
     }

