filtermirnapath          package:miRNApath          R Documentation

_F_i_l_t_e_r _m_i_R_N_A_p_a_t_h _d_a_t_a

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

     This method filters the miRNApath data to denote hits versus
     non-hits, the required distinction for running the enrichment
     algorithm. Data is expected to have been loaded by the
     'loadmirnapath' method.

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

     filtermirnapath(mirnaobj, pvalue=NA, expression=NA, foldchange=NA)

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

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

  pvalue: If a p-value column has been defined in the mirnapath object,
          this value is used to define a subset of entries within the
          dataset which will be denoted as hits. 

expression: If an expression column has been defined in the mirnapath
          object, this value will be used to define entries with
          expression above this expression level as hits. 

foldchange: If a fold change column has been defined in the mirnapath
          object, this value is used to require hits to have a fold
          change greater than or equal to this value. The fold change
          is evaluated in both the positive and the negative, such that
          a foldchange=2 will allow foldchange=2 and foldchange=-2. 

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

     This method takes a mirnapath object and assigns a flag for hits
     and non-hits, depending upon what filter criteria was provided. If
     multiple criteria are provided, they will all be collectively
     applied such that all criteria must be fulfilled. To that end,
     multiple calls to this function on the same mirnapath object
     should successively shrink the list of hits dependent upon the
     given criteria.

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

     Object of type mirnapath. The state of the object will reflect
     that the data has been filtered.

_N_o_t_e:

     The method attempts to convert fold change columns appropriately
     so that filtering by 2 will properly mark entries greater than 2,
     less than -2, or less than 0.5, as the case may be.

_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:

     ## Load miRNA expression data from AD miRNA paper
     ## This data contains miRNA expression data, 
     data(mirnaobj);

     ## Display the state, which should generally be "unfiltered"
     ## at this point
     mirnaobj@state;

     ## Display summary information about the object
     mirnaobj;

     ## Annotate hits by filtering by P-value 0.05
     mirnaobj <- filtermirnapath( mirnaobj, pvalue = 0.05,
         expression = NA, foldchange = NA );

     ## Display summary, noting the state is "filtered"
     mirnaobj;

