exonStructure         package:GeneRegionScan         R Documentation

_A_d_d _e_x_o_n-_s_t_r_u_c_t_u_r_e _t_o _p_l_o_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     Function that will paint the exon structure of a gene on the plots
     obtained by plotOnGene.

_U_s_a_g_e:

         exonStructure(mrna, genome, maxMismatch=4)

_A_r_g_u_m_e_n_t_s:

    mrna: A gene sequence formatted as DNAstring, character-vectors or
          readFASTA output.

  genome: A number of gene sequences as DNAstring, vectors of
          DNAStrings, character-vectors or readFASTA outputs.

maxMismatch: Integer. The maximum number of mismatches per exon that
          can be allowed before the exon is not allocated at the
          position in the template mrna. Defaults to 4.

_D_e_t_a_i_l_s:

     When given a sequence of the DNA divided by exons and a sequence
     of the corresponding mRNA string, this function will plot the
     layout of exons along the length of the x-axis on the current
     device. The sequences have to be given as FASTA sequences produced
     by the readFASTA function in the Biostrings package. Furthermore
     the genome must be divided with an entry for each exon. This is
     easily done by downloading the genome sequences of the
     gene-of-interest from http://genome.ucsc.edu and specifying "One
     FASTA record per region".

     The function works by sequentially comparing each exon to the
     mrna. The location of the match start and end is taken as the exon
     boundaries and plotted. If more than one match is found a warning
     is given. If no match is found for an exon this is printed, but
     otherwise ignored. The mrna can in fact also be DNA sequence with
     introns. The important thing  is that it serves as template for
     the exon matching.

     Importantly, the exon-numbers technically refer to "number of exon
     in investigated transcript". For example if  an DNA with exon
     structure for an isoform which does not include all exons in the
     gene is investigated, then there will  be skips of exon numbers.
     To avoid this, the DNA for an isoform which do include all exons
     could be used.  However, it is really more a biological issue:
     different sources can differ on where to start  the counting for a
     given gene in any case.

_V_a_l_u_e:

     No value, but plots the layout of exons in a gene on the product
     of a call to plotOnGene.

_A_u_t_h_o_r(_s):

     Lasse Folkersen

_S_e_e _A_l_s_o:

     'geneRegionScan', 'plotOnGene'

_E_x_a_m_p_l_e_s:

             data(exampleProbeLevelSet)
             plotOnGene(exampleProbeLevelSet, mrna, label="gender", testType="wilcoxon")
             exonStructure(mrna, genomic, maxMismatch=2)

