activeMod             package:maigesPack             R Documentation

_F_u_n_c_t_i_o_n_a_l _c_l_a_s_s_i_f_i_c_a_t_i_o_n _o_f _g_e_n_e _g_r_o_u_p_s

_D_e_s_c_r_i_p_t_i_o_n:

     This function calculate profiles of expression for groups of genes
     in each sample of the dataset and for each biological condition
     (group of samples).

_U_s_a_g_e:

     activeMod(data=NULL, gNameID="GeneName", samples=NULL, usePaths=FALSE,
               sLabelID="Classification", adjP="none", cutExp=1,
               cutPhiper=0.05)

_A_r_g_u_m_e_n_t_s:

    data: object of class 'maiges' to be used to functionally classify
          gene groups stored in 'GeneGrps' slot.

 gNameID: character string specifying identification of gene label to
          be used. 

sLabelID: idem to the previous argument for identification of sample
          label.

 samples: a list with character vectors specifying the groups that must
          be compared.

usePaths: logical specifying if the pathways given in 'Paths' slot must
          also be used, defaults to FALSE.

  cutExp: real number specifying the cutoff for expression levels (to
          discretise the expression)

    adjP: character string giving the type of p-value adjustment. May
          be 'Bonferroni', 'Holm', 'Hochberg', 'SidakSS', 'SidakSD',
          'BH', 'BY' or 'none'. Defaults to 'none'. See function
          'mt.rawp2adjp' in package multtest for more details.

cutPhiper: p-value cutoff to select significant gene groups.

_D_e_t_a_i_l_s:

     If the argument 'samples' is NULL, all types defined by the sample
     label given by 'sLabelID' are used. It is possible to use the
     'plot.maigesActMod' and 'image.maigesActMod' to display the
     results of this analysis. This function is based in the method
     proposed by Segal et al. (2004).

_V_a_l_u_e:

     The result of this function is an object of class 'maigesActMod'.

_A_u_t_h_o_r(_s):

     Gustavo H. Esteves <gesteves@vision.ime.usp.br>

_R_e_f_e_r_e_n_c_e_s:

     Segal, E.; Friedman, N.; Koller, D. and Regev, A. A module map
     showing conditional activity of expression modules in cancer.
     *Nature Genetics*, 36, 1090-1098, 2004. (<URL:
     http://www.nature.com/ng/journal/v36/n10/abs/ng1434.html>)

_S_e_e _A_l_s_o:

     'activeModScoreHTML', 'maigesActMod', 'plot.maigesActMod',
     'image.maigesActMod', 'mt.rawp2adjp'

_E_x_a_m_p_l_e_s:

     ## Loading a little dataset
     data(gastro)

     ## Doing functional classification of gene groups for 'Tissue' sample label
     gastro.mod = activeMod(gastro.summ, sLabelID="Tissue", cutExp=1,
       cutPhiper=0.05)

     ## Doing functional classification of gene groups together with the
     ## networks given by Paths slot for 'Tissue' sample label. Also we are
     ## using a cuttoff for p-value of hipergeometric test as 0.1
     gastro.mod = activeMod(gastro.summ, sLabelID="Tissue", cutExp=1,
       cutPhiper=0.1, usePaths=TRUE)

