dabg.call                package:xps                R Documentation

_D_e_t_e_c_t_i_o_n _A_b_o_v_e _B_a_c_k_g_r_o_u_n_d _C_a_l_l

_D_e_s_c_r_i_p_t_i_o_n:

     Computes the Detection Above Background Call first implemented for
     the Exon arrays.

_U_s_a_g_e:

     dabg.call(xps.data, filename = character(0), filedir = getwd(),
               alpha1 = 0.04, alpha2 = 0.06,
               option = "transcript", exonlevel = "", xps.scheme = NULL, add.data = TRUE, verbose = TRUE)

     xpsDABGCall(object, ...)

_A_r_g_u_m_e_n_t_s:

xps.data: object of class 'DataTreeSet'.

filename: file name of ROOT data file.

 filedir: system directory where ROOT data file should be stored.

  alpha1: a significance threshold in (0,alpha2).

  alpha2: a significance threshold in (alpha1,0.5).

  option: option determining the grouping of probes for summarization,
          one of  'transcript', 'exon', 'probeset'; exon arrays only.

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

xps.scheme: optional alternative 'SchemeTreeSet'.

add.data: logical. If 'TRUE' call data will be added to slots 'data'
          and 'detcall'.

 verbose: logical, if 'TRUE' print status information.

  object: object of class 'DataTreeSet'.

     ...: the arguments described above.

_D_e_t_a_i_l_s:

     This function generates a detection p-value based on comparing the
     perfect match probe intensity to the intensity distribution
     provided by background probes sharing the same GC-content as the
     PM probe under consideration. For exon/genome arrays special
     'antigenomic' background probes of defined GC-content are used,
     while for expression arrays the Mismatch probes will be grouped by
     their GC-content. 

     For exon/genome arrays it is necessary to supply 'option' and
     'exonlevel'.

     Following 'option's are valid for exon arrays only:

       'transcript':  expression levels are computed for transcript clusters, i.e. probe sets containing the same 'transcript_cluster_id'.
       'exon':        expression levels are computed for exon clusters, i.e. probe sets containing the same 'exon_id', where each exon cluster consists of one or more 'probeset's.
       'probeset':    expression levels are computed for individual probe sets, i.e. for each 'probeset_id'.

     Following 'exonlevel' annotations are valid for exon arrays:

         '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.
         'ambiguous':     ambiguous probesets only.
         'affx':          standard AFFX controls.
         'all':           combination of above.

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

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

     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'.

     In order to use an alternative 'SchemeTreeSet' set the
     corresponding SchemeTreeSet 'xps.scheme'.

     'xpsDABGCall' is the 'DataTreeSet' method called by function
     'dabg.call',  containing the same parameters.

_V_a_l_u_e:

     A 'CallTreeSet'

_N_o_t_e:

     Yes, it is possible to compute DABG detection call for expression
     arrays, but it is very slow and thus not recommended.

_A_u_t_h_o_r(_s):

     Christian Stratowa

_R_e_f_e_r_e_n_c_e_s:

     Affymetrix (2005) Exon Probeset Annotations and Transcript Cluster
     Groupings, Affymetrix Inc.,  Santa Clara, CA,
     exon_probeset_trans_clust_whitepaper.pdf.

_S_e_e _A_l_s_o:

     'mas5.call'

_E_x_a_m_p_l_e_s:

     ## first, load 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="/"))

     ## DABG detection call
     call.dabg <- dabg.call(data.test3,"tmp_Test3DABG",verbose=FALSE)

     ## get data.frames
     pval.dabg <- pvalData(call.dabg)
     pres.dabg <- presCall(call.dabg)
     head(pval.dabg)
     head(pres.dabg)

     ## plot results
     if (interactive()) {
     callplot(call.dabg)
     }

     rm(scheme.test3, data.test3)
     gc()

