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)

