splanova               package:exonmap               R Documentation

_F_i_n_d _p_r_o_b_e_s_e_t_s _i_n_v_o_l_v_e_d _i_n _d_i_f_f_e_r_e_n_t_i_a_l _s_p_l_i_c_i_n_g _f_o_r _m_u_l_t_i_p_l_e _t_r_e_a_t_m_e_n_t_s

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

     Reads expression data and using its 'pData'  calculates F-values
     and finds significant cases using ANOVA.  The approach is similar
     to MIDAS, described in Affymetrix white  paper "Alternative
     Transcript Analysis Methods for Exon Arrays".

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

     splanova (x,genesin, group,base, thr=0.05, probes.min=4, exonic=T, debug=0)
     fval(object)
     sig(object)

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

       x: eSet for which splicing is to be calculated 

 genesin: Vector of Ensembl gene names to check 

   group: Group name from covdesc 

    base: Reference treatment name for the one-way ANOVA model - must
          be in the group in covdesc 

     thr: Alpha level threshold for F-test 

probes.min: Minimal number of probes to include the probeset in the
          search - see 'gene.to.probeset'

  exonic: Specifies if only exonic probesets should be used - see
          'select.probewise'

   debug: Debug level - 0 stands for no debug messages 

  object: a splanova object of class 'Splanova'

_D_e_t_a_i_l_s:

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

     A Splanova object with two slots : fval - list of F-values from
     ANOVA and sig - descriptive  listing of splicing events.

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

     Michal J Okoniewski

_R_e_f_e_r_e_n_c_e_s:

     <URL:  http://bioinformatics.picr.man.ac.uk/>

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

     'splicing.index', code{gene.to.probeset}, 'select.probewise',
     'pData  '

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

      
       ## Not run: 
         gg <- probeset.to.gene(c("2326780","2326822" ))
         spl.multi <-  splanova(x.rma, gg, "group", "a", thr=0.05, debug=4)
         fval(spl.multi)
         sig(spl.multi)
       
     ## End(Not run)

