features2Probes            package:Ringo            R Documentation

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

     This function creates a mapping between annotated genomic features
     and probes on the array whose matching genomic positions are
     stored in a probeAnno environment.

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

     features2Probes(gff, probeAnno, upstream = 5000, checkUnique = TRUE, uniqueCodes = c(0), mem.limit=1e8, verbose = TRUE)

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

     gff: 'data.frame' holding genomic feature annotation

probeAnno: Object of class 'environment' holding the genomic positions
          of probes in the ExpressionSet

upstream: up to how many bases upstream of annotated genomic features
          should probes be counted as related to that feature (see
          details)

checkUnique: logical; indicates whether the uniqueness indicator of
          probe matches from the probeAnno environment should be used.

uniqueCodes: numeric; which numeric codes in the chromosome-wise
          match-uniqueness elements of the probeAnno environment
          indicate uniqueness?

mem.limit: integer value; what is the maximal allowed size of matrices
          during the computation; see 'regionOverlap'

 verbose: logical; detailed progress output to STDOUT?

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

     The results is a list of length equal to the number of rows in the
     provided 'gff', the data.frame of genomic features. The 'names' of
     the list are the names specified in the 'gff'. Each element of the
     list is specified by the probes mapping into the genomic region
     from 'upstream' bases upstream of the feature's start site to the
     feature's end site. The entries itself are either 'NULL', if no
     probe was mapped into this region, or a named numeric vector, with
     its values being the distances of the probes' middle positions to
     the feature's start site (which depends on the strand the feature
     is on) and its names being the identifiers of these probes.

_N_o_t_e:

     This resulting mapping is not used excessively by other Ringo
     functions, so creating this mapping is optional at this time, but
     it may simplify subsequent gene/transcript-based analyses.

     Here, the term _feature_ describes a genomic entity such as a
     gene, transcript, non-coding RNA or a similar feature annotated to
     a genome. It does NOT refer to oligo-nucleotide or cDNA probes on
     the microarray.

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

     Joern Toedling toedling@ebi.ac.uk

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

     'regionOverlap'

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

        ringoExampleDir <- system.file("exData",package="Ringo")
        load(file.path(ringoExampleDir,"exampleProbeAnno.rda"))
        trans2Probe <- features2Probes(exGFF, exProbeAnno)
        trans2Probe[exGFF$name[match("NUDT2", exGFF$symbol)]]
        exGFF[match(names(trans2Probe)[listLen(trans2Probe)>0],exGFF$name),]
        trans2Probe[listLen(trans2Probe)==1]

