deGenes2by2BootT         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 a bootstrap of t statistics method.

_U_s_a_g_e:

     deGenes2by2BootT(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 t statistics and p-values by re-sampling
     of the data using the function 'bootstrapT'.

     There is the option to do the t test directly, using the function
     'deGenes2by2Ttest', or to do the non-parametric Wilcox test using
     the function 'deGenes2by2Wilcox'.

_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:

     'bootstrapT', 'deGenes2by2Ttest' and 'deGenes2by2Wilcox'.

_E_x_a_m_p_l_e_s:

     ## Loading the dataset
     data(gastro)

     ## Doing bootstrap from t statistic test fot 'Type' sample label, k=1000
     ## specifies one thousand bootstraps
     gastro.boot = deGenes2by2BootT(gastro.summ, sLabelID="Type", k=1000)
     gastro.boot

