deGenes2by2Wilcox         package:maigesPack         R Documentation

_F_u_n_c_t_i_o_n _t_o _d_o _d_i_f_f_e_r_e_n_t_i_a_l _e_x_p_r_e_s_s_i_o_n _a_n_a_l_y_s_i_s, _c_o_m_p_a_r_i_n_g _o_n_l_y _t_w_o
_s_a_m_p_l_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     This function takes an object of class 'maiges' and do
     differential expression analysis for the genes onto dataset,
     comparing only two samples, by the Wilcox (Mann-Withney) test.

_U_s_a_g_e:

     deGenes2by2Wilcox(data=NULL, sLabelID=names(data@Slabels)[1], sTypeComp=NULL,
                       doClust=TRUE, ...)

_A_r_g_u_m_e_n_t_s:

    data: object of class 'maiges'.

sLabelID: character string giving the sample label ID to be used.

sTypeComp: list with character vectors specifying the two sample types
          to be compared.

 doClust: logical indicating if the object generated from this analysis
          will be used for cluster analysis. Defaults to TRUE.

     ...: additional parameters for functions 't.test', 'wilcox.test'
          or 'bootstrapT'.

_D_e_t_a_i_l_s:

     This function calculate Wilcox statistics and p-values for the
     test comparing the equality of means using the function
     'wilcox.test'.

     There another function to do parametric t test ,
     'deGenes2by2Ttest', and another option of non-parametric test
     doing bootstrap of t statistics, 'deGenes2by2BootT'.

_V_a_l_u_e:

     The result of this function is an object of class 'maigesDE' if
     'doClust' if FALSE or of class 'maigesDEcluster' if it is TRUE.

_A_u_t_h_o_r(_s):

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

_S_e_e _A_l_s_o:

     'wilcox.test', 'deGenes2by2Ttest' and 'deGenes2by2BootT'.

_E_x_a_m_p_l_e_s:

     ## Loading the dataset
     data(gastro)

     ## Doing wilcoxon test fot 'Type' sample label
     gastro.wilcox = deGenes2by2Wilcox(gastro.summ, sLabelID="Type")
     gastro.wilcox

