pm-methods                package:xps                R Documentation

_M_e_t_h_o_d_s _f_o_r _a_c_c_e_s_s_i_n_g _p_e_r_f_e_c_t _m_a_t_c_h_e_s _a_n_d _m_i_s_m_a_t_c_h_e_s

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

     Methods for accessing perfect match (PM) and mismatch (MM) probes.

     _Usage_

     'pm(object, which = "pm")'

     'mm(object, which = "mm")'

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

  object: object of class 'DataTreeSet'.

   which: type of perfect match or mismatch probes to be returned.

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

     For expression arrays all the perfect match (pm) or mismatch (mm)
     probes on the arrays  the object represents are returned as
     data.frame.

     For exon arrays, 'pm' returns the probes of the different exon
     levels as data.frame,  i.e. 'which' can have one of the following
     values:

         'core':          probesets supported by RefSeq and full-length GenBank transcripts.
         'metacore':      core meta-probesets.
         'extended':      probesets with other cDNA support.
         'metaextended':  extended meta-probesets.
         'full':          probesets supported by gene predictions only.
         'metafull':      full meta-probesets.
         'affx':          standard AFFX controls.

     For whole genome arrays, 'pm' returns the probes of the different
     exon levels as data.frame,  i.e. 'which' can have one of the
     following values:

         'core':      probesets with category unique and mixed.
         'metacore':  probesets with category unique only.
         'affx':      standard AFFX controls.

     For exon/genome arrays, 'mm' returns the background probes as
     data.frame,  i.e. 'which' is either genomic or antigenomic.

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

     A 'data.frame'.

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

     Christian Stratowa

_S_e_e _A_l_s_o:

     'validData'

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

     ## load existing ROOT scheme file and ROOT data file
     scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
     data.test3 <- root.data(scheme.test3, paste(.path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))

     ## need to attach scheme mask and probe intensities
     data.test3 <- attachMask(data.test3)
     data.test3 <- attachInten(data.test3)

     pm <- pm(data.test3)
     mm <- mm(data.test3)
     head(pm)
     head(mm)

     ## optionally remove mask and data to free memory
     data.test3 <- removeInten(data.test3)
     data.test3 <- removeMask(data.test3)

