mirnaobj              package:miRNApath              R Documentation

_m_i_r_n_a_o_b_j, _a_n _S_4 _o_b_j_e_c_t _o_f _c_l_a_s_s "_m_i_r_n_a_p_a_t_h"

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

     An example miRNApath data object containing miRNA data, gene  and
     pathway associations. The object represents the end result of the
     miRNApath workflow, and serves a convenient source for example
     data.

_U_s_a_g_e:

     data(mirnaobj)

_F_o_r_m_a_t:

     The format is an S4 class '"mirnapath"' with 'slotNames' as
     follows:


      '_m_i_r_n_a_T_a_b_l_e'  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'  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'  Numerical value indicating how many sample groups
          are available in the data, provided for convenience.

      '_s_t_a_t_e'  Character value 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'  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'  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'  Numerical value indicating how many pathways are
          available in the data, provided for convenience.

      '_f_i_l_t_e_r_s'  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'  Named list of 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.

_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:

     ## Load the data
     data(mirnaobj)

     ## Print the default summary
     mirnaobj;

