exonLevel                package:xps                R Documentation

_C_o_n_v_e_r_s_i_o_n _o_f _P_a_r_a_m_e_t_e_r _e_x_o_n_l_e_v_e_l _t_o _I_n_t_e_g_e_r

_D_e_s_c_r_i_p_t_i_o_n:

     Conversion of parameter 'exonlevel' to an integer vector.

_U_s_a_g_e:

     exonLevel(exonlevel = "", chiptype = "GeneChip", as.sum = TRUE)

_A_r_g_u_m_e_n_t_s:

exonlevel: exon annotation level determining which probes should be
          used for summarization; exon/genome arrays only.

chiptype: chip tpye, one of 'GeneChip', 'GenomeChip', 'ExonChip'.

  as.sum: logical, if 'TRUE' an integer vector of size three will be
          returned, if  'FALSE' then the levels will be split into the
          basic integer representations.

_D_e_t_a_i_l_s:

     Conversion of parameter 'exonlevel' to an integer; this function
     is a utility function, which is usually only used internally.

     Following 'exonlevel' annotations are valid for exon arrays:

         'core':          '(=8192+1024)' probesets supported by RefSeq and full-length GenBank transcripts.
         'metacore':      '(=8192)' core meta-probesets.
         'extended':      '(=4096+512)' probesets with other cDNA support.
         'metaextended':  '(=4096)' extended meta-probesets.
         'full':          '(=2048+256)' probesets supported by gene predictions only.
         'metafull':      '(=2048)' full meta-probesets.
         'ambiguous':     '(=128)' probesets that fall within multiple genes.
         'affx':          '(=60)' standard AFFX controls.
         'all':           '(=16316)' combination of above (including affx).

     Following 'exonlevel' annotations are valid for whole genome
     arrays:

         'core':      '(=8192+1024)' probesets with category 'unique', 'similar' and 'mixed'.
         'metacore':  '(=8192)' probesets with category 'unique' only.
         'affx':      '(=60)' standard AFFX controls.
         'all':       '(=9276)' combination of above (including affx).

     Exon levels can also be combined, with following combinations
     being most useful:

       'exonlevel="metacore+affx"':       core meta-probesets plus AFFX controls
       'exonlevel="core+extended"':       probesets with cDNA support
       'exonlevel="core+extended+full"':  supported plus predicted probesets

     Exon level annotations are described in the Affymetrix whitepaper
     exon_probeset_trans_clust_whitepaper.pdf: 
       "Exon Probeset Annotations and Transcript Cluster Groupings".

     Parameter 'exonlevel' determines not only which probes are used
     for medianpolish, but also the probes used for background
     calculation and for quantile normalization. If you want to use
     seperate probes for background calculation, quantile normalization
     and medianpolish summarization, you can pass a numeric vector
     containing three integer values corresponding to the respective 
     'exonlevel'. These integers must be the sum of the integers shown
     above, e.g. you can use  'exonlevel=c(16316,8252,8252)', where
     '8252=8192+60' for '"metacore+affx"'.

_V_a_l_u_e:

     an 'integer' vector.

_A_u_t_h_o_r(_s):

     Christian Stratowa

_S_e_e _A_l_s_o:

     'rma', 'mas5'

_E_x_a_m_p_l_e_s:

     exonLevel("core", "GenomeChip")
     exonLevel("all", "GenomeChip")
     exonLevel("core+extended+full", "ExonChip")
     exonLevel("core+extended+full", "ExonChip", as.sum=FALSE)
     exonLevel(c(16316,8252,8252), "ExonChip")

