mirnapath-class          package:miRNApath          R Documentation

_S_4 _c_l_a_s_s _m_i_r_n_a_p_a_t_h _a_n_d _i_t_s "_s_h_o_w" _m_e_t_h_o_d

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

     miRNApath class intended to contain miRNA data, gene and pathway
     associations, and ultimately the pathway enrichment results in
     detail.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new("mirnapath",
     ...)'.

_S_l_o_t_s:


      '_m_i_r_n_a_T_a_b_l_e': Object of class '"data.frame"', containing the
          miRNA results data, expected to contain columns with miRNA
          name, gene name, and ideally some column(s) for filtering
          hits versus background, e.g. fold change, expression
          abundance, P-value. Once the data is filtered (see state
          below) there will be a column with a flag indicating which
          entries are hits and which are considered background. This
          column is found in  'mirnaobj@columns["filterflagcolumn"]'
          and is typically '"FILTERFLAG"'.

      '_c_o_l_u_m_n_s': Object of class '"character"', Named list of column
          headers used throughout the analysis. The purpose of the
          names is partly to retain the original headers in the
          mirnaTable data.frame, and partly to coordinate the names
          with the miRNA-gene and gene-pathway tables used later in the
          analysis. The recognized headers: 'mirnacol, assayidcol,
          genecol, pvaluecol, foldchangecol, pathwaycol, pathwayidcol,
          groupcol, mirnagene'. See the documentation for the mirnapath
          object type for more details about usage.

      '_g_r_o_u_p_c_o_u_n_t': Object of class '"numeric"', indicating how many
          sample groups are available in the data, provided for
          convenience.

      '_s_t_a_t_e': Object of class '"character"', indicating the current
          analysis state, with values: '"unfiltered"' if results are
          loaded but not yet filtered; '"filtered"' if results are
          loaded and hits are defined with the filterflagcol column;
          '"enriched"' if the data is loaded, filtered, and analyzed
          for enrichment. One can load mirna-gene and gene-pathway data
          at any point which necessitates using the
          'mirnaobj@mirnaGene' or 'mirnaobj@mirnaPathways' object
          elements to determine if that data has been loaded.

      '_m_i_r_n_a_G_e_n_e': Object of class '"data.frame"', containing
          associations between miRNA and genes. The data should contain
          one miRNA-to-gene relationship per row, and should contain
          only those two columns. Additional columns are maintained but
          ignored. Note that one can use any values in the genecol
          column, provided they match exactly with values found in the
          'mirnaobj@mirnaPathways' element (see below.) Therefore, if
          desired one can use transcript or gene associations, or other
          integration methods as desired.

      '_m_i_r_n_a_P_a_t_h_w_a_y_s': Object of class '"data.frame"', containing
          gene-pathway associations. The data should contain only one
          gene-to-pathway association per row of data. The data can
          have pathway ID values, which may facilitate comparisons to
          pathway databases (and may allow substantial data volume
          reduction if necessary.) If there is no pathwayidcol column,
          then one will be created using a numerical assignments of the
          pathway names. Note that this conversion is not sensitive to
          pathway sources, so care should be taken to include pathway
          source in the pathway name if two sources share the same
          pathway name. The same is true for pathway ID values, should
          they be purely numerical and have shared values across
          pathway sources.

      '_p_a_t_h_w_a_y_c_o_u_n_t': Object of class '"numeric"', Numerical value
          indicating how many pathways are available in the data,
          provided for convenience.

      '_f_i_l_t_e_r_s': Object of class '"numeric"', List of filters applied
          to the data, which may include: '"P-value", "Fold change"',
          and/or '"Expression"'.

      '_e_n_r_i_c_h_m_e_n_t': Enrichment summary data in the form of a list of
          elements for each sample group (the sample group is the name
          of each element.) Each list element is itself a list with
          enrichment result data for each sample group, as
          independently calculated: '"pvalues"' - list of P-values
          named by pathway ID; '"Measured pathway mirnaGenes"' - total
          number of miRNA-gene-pathway combinations measured, which
          gives some idea of the overall coverage of pathways. The
          general point is that miRNAs have the potential to cover many
          genes and pathways; '"Total mirnaGenes"' - number of
          miRNA-gene combinations represented in the data; '"Enriched
          pathway mirnaGenes"' - number of miRNA-gene values enriched
          in the pathway tested; '"Enriched by miRNA"' - list of miRNAs
          involved in the pathway tested, with the list of genes in
          parentheses per miRNA; '"Enriched by Gene"' - same as
          previous except switching gene and miRNA; '"Total enriched
          mirnaGenes"' - the total number of miRNA-gene values involved
          in any pathway enrichment (significant or not.) The total
          values are useful when comparing across sample groups,
          looking particularly for groups with few changes or those
          with a uniquely high number of changes.

      '_p_a_t_h_w_a_y_L_i_s_t': Object of class '"character"', pathways contained
          in the 'mirnaobj@mirnaPathways' object, named by the pathway
          ID values found in the pathwayidcol column. This list
          facilitates converting the data in the enrichment element to
          pathway names, since those values are named by the pathway ID
          to conserve memory.

_M_e_t_h_o_d_s:


     _s_h_o_w 'signature(object = "mirnapath")': ... 

_S_o_u_r_c_e:

     Journal of Alzheimers Disease 14, 27-41.

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

     John Cogswell (2008) Identification of miRNA changes in
     Alzheimer's disease brain and CSF yields putative  biomarkers and
     insights into disease pathways, Journal of Alzheimer's Disease 14,
     27-41.

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

     library(miRNApath);

     data(mirnaobj);

     # the slotNames and definitions are described
     #showClass(mirnaobj);

     # Default "show" method describes the contents of the object
     mirnaobj;

