tablesDE             package:maigesPack             R Documentation

_S_a_v_e _H_T_M_L _o_r _C_S_V _t_a_b_l_e_s _o_f _d_i_f_f_e_r_e_n_t_i_a_l_l_y _e_x_p_r_e_s_s_e_d _g_e_n_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     This function takes an object of class 'maigesDE' or
     'maigesDEcluster' generated by functions 'deGenes2by2Ttest',
     'deGenes2by2Wilcox', 'deGenes2by2BootT' and 'deGenesANOVA' and
     save HTML or CSV tables differentially expressed genes.

_U_s_a_g_e:

     tablesDE(deComp=NULL, dir="./", filenames=NULL, dataID="Someone's",
              type=c("HTML","CSV")[1], geneID="GeneName", hsID="ClusterId",
              gbID="GeneId", annotID="Annot", genes=NULL, logFold=TRUE,
              adjP="none", sort="p.value", nDEgenes=NULL)

_A_r_g_u_m_e_n_t_s:

  deComp: object of class 'maigesDE'.

     dir: character specifying the directory to save the files.

filenames: character vector with file names to be saved, if NULL
          default names are given.

  dataID: character giving an identifier for the dataset. If NULL the
          'notes' slot from 'DE.comp' are used.

    type: type of file to be saved. May be 'HTML' (default) or 'CSV'.

  geneID: character giving the ID of label  for gene symbol in the
          dataset.

    hsID: character giving the ID of label for unigene code in the
          dataset.

    gbID: character giving the ID of label for Genbank entry in the
          dataset.

 annotID: character giving the ID of label for gene annotation in the
          dataset.

   genes: character vector specifying the genes to be saved, mapped
          according to 'geneID' label.

 logFold: logical specifying if the fold change must be saved in log2
          scale.

    adjP: character string giving the type of p-value adjustment. May
          be 'Bonferroni', 'Holm', 'Hochberg', 'SidakSS', 'SidakSD',
          'BH', 'BY' or 'none'. Defaults to 'none'.

    sort: character specifying the field to be sorted, may be 'p.value'
          (default), 'fold' or 'statistic'. 

nDEgenes: number of differentially genes to be saved in the file.
          Defaults to NULL to save all genes. If an integer value the
          function saves the 'nDEgenes' with smaller p-values (most
          significantly DE genes). If a number in (0,1) 'nDEgenes' is
          used as a cutoff for the p-values.

_D_e_t_a_i_l_s:

     We use the function 'mt.rawp2adjp' from package _multtest_ to
     adjust p-values, any information the methods implemented must be
     searched in their help pages. The arguments 'hsID', 'gbID' and
     'annotID' are used only to improve the tables generate including
     links for the respective databases, but if these information are
     absent in the dataset they must be specified as NULL. The argument
     'geneID' must be necessarily specified, because the genes must be
     at least one identification.

_V_a_l_u_e:

     This function don't return any object.

_A_u_t_h_o_r(_s):

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

_S_e_e _A_l_s_o:

     'deGenes2by2Ttest', 'deGenes2by2Wilcox', 'deGenes2by2BootT',
     'deGenesANOVA', 'maigesDE', 'maigesDEcluster'.

_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.ttest = deGenes2by2Ttest(gastro.summ, sLabelID="Type")

     tablesDE(gastro.ttest) ## Save HTML tables

     ## To save only tables with p-value < 0.05
     tablesDE(gastro.ttest, nDEgenes=0.05)

     ## To save only tables with 30 most significantly genes
     tablesDE(gastro.ttest, nDEgenes=30)

