runEnrichment           package:miRNApath           R Documentation

_P_e_r_f_o_r_m _g_e_n_e _s_e_t _e_n_r_i_c_h_m_e_n_t _a_n_a_l_y_s_i_s _o_n _a _m_i_R_N_A_p_a_t_h 
_o_b_j_e_c_t

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

     This method performs a hypergeometric enrichment analysis on a
     miRNApath object, which should already contain miRNA data,
     miRNA-gene associations, gene-pathway associations, and some
     criteria for filtering miRNA hits from the full tested set.

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

     runEnrichment(mirnaobj, Composite=TRUE, groups=NULL,
     permutations=0)

_A_r_g_u_m_e_n_t_s:

mirnaobj: An object of type mirnapath containing data resulting from
          the 'loadmirnapath' method. 

Composite: Defines whether the enrichment treats miRNA-gene as the
          enriched entity, or uses only the gene. 

  groups: List of groups to include in the analysis, although each
          group is analyzed independent from the other groups. 

permutations: The number of permutations to use in calculating an
          adusted P-value. Value of 0 will perform no permutations. 

_D_e_t_a_i_l_s:

     The composite flag indicates whether to treat the fully  expanded
     miRNA-gene combinations as separate enrichment events (TRUE), or
     whether to treat all effects on one gene as one collective event.
     The latter case reverts to the classic un-ordered hypergeometric
     enrichment technique.

     However the expansion of combinations is the current method chosen
     to represent the multiple predicted effects of miRNAs to one gene,
     and the predicted effect of one miRNA to multiple genes. The
     algorithm will identify statistically significantly enriched
     results when the combination of these effects is greater than
     would be anticipated by random chance.

     The adjusted P-value is calculated using the rank of unadjusted
     P-values divided by the number of permutations minus one (such
     that the best rank from 1,000 permutations yields an adjusted
     P-value of 0.001.) The default value 0 was put in place to save
     time, since most adjustments resulted in stronger "hits" and
     weaker "non-hits" in terms of pathways enriched. Thus the results
     are not substantially changed, and permutation adjustment is saved
     for the final result set.

_V_a_l_u_e:

     The method returns an object of type mirnapath, a list with
     components:

 mirnaTable : data.frame containing the miRNA results data 

 columns : list containing the names of required column headers
          associated to the actual column header supplied in the
          dataset contained in mirnaTable. Required headers: mirnacol,
          assayidcol, groupcol, filterflagcol. 

 groupcount : The number of groups contained in mirnaTable using the
          groupcol, if supplied 

  state : The current state of the object, in this case "enriched". 

 mirnaGene : data.frame containing associations between miRNAs and
          genes. 

 mirnaPathways : data.frame containing gene-pathway associations. 

 pathwaycount : Numerical value indicating how many pathways are
          available in the data, provided for convenience. 

 filters : List of filters applied to the data, which may include:
          "P-value", "Fold change", and/or "Expression". 

 enrichment : 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. Lastly, with permutations > 0 "Permutation
          P-value" will contain the rank-adjusted P-value as described
          in the details section. 

 pathwayList : 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. 

_A_u_t_h_o_r(_s):

     James M. Ward jmw86069@gmail.com

_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.

_S_e_e _A_l_s_o:

     'loadmirnapath', 'filtermirnapath', 'loadmirnatogene',
     'loadmirnapathways'

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

     ## Not run: 
     ## Start with miRNA data from this package
     data(mirnaobj);

     ## Now run enrichment test
     mirnaobj <- runEnrichment( mirnaobj=mirnaobj, Composite=TRUE,
        groups=NULL, permutations=0 );
     ## End(Not run)

