loadmirnapath           package:miRNApath           R Documentation

_L_o_a_d _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 loads data from a tab-delimited flatfile into an
     object of type mirnapath to be used for further miRNA analysis.

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

     loadmirnapath(mirnafile="mirna_input.txt", mirnacol="miRNA Name",
         assayidcol="ASSAYID", groupcol="GROUP", 
         filterflagcol="FILTERFLAG", expressioncol=NA, 
         foldchangecol=NA, pvaluecol=NA)

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

mirnafile: The tab-delimited miRNA results file to be loaded. The file
          is expected to be in tall-skinny format. 

mirnacol: The name of the column header which contains the miRNA names
          being assayed. 

assayidcol: The name of the column containing values which distinguish
          different assays for the same miRNA. 

groupcol: The (optional) name of the column which contains sample group
          information. Enrichment is run separately for each sample
          group, defining a unique universe for the basis of the
          enrichment. 

filterflagcol: The column header which does or will contain a flag
          distinguishing hits from non-hits. This column is typically
          not supplied and is created during the  'filtermirnapath'
          step. 

expressioncol: The (optional) column header for values containing the
          expression abundances of the miRNAs assayed. 

foldchangecol: The (optional) column header for values containing the
          fold changes of the miRNAs assayed. 

pvaluecol: The (pvaluecol) column header for values containing the
          P-values of the miRNAs assayed. 

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

     This method is the primary means for loading data into the
     miRNApath package.

     Data is not assumed to have any particular numerical values,
     however the basic column types are typically used: expression
     abundance, fold change, and P-value. Should one or more columns be
     specified and available, it will be available for filtering later
     on with 'filtermirnapath'.

     The group column assumes there is one column containing all sample
     group information.

     The assayid column is used to distinguish multiple assays for the
     same miRNA, such as different vendors, or even different
     preparations of the same miRNA assay.

_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. Optional headers: groupcol, pvaluecol,
          foldchangecol, expressioncol, filterflagcol 

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

  state : the current state of the object, using the following values
          in order of progress through the typical workflow:
          unfiltered, filtered, enriched. 

_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:

     ## Start with miRNA data from this package
     data(mirnaobj);

     ## Write a file as example of required input
     write.table(mirnaobj@mirnaTable, file = "mirnaobj.txt", 
         quote = FALSE, row.names = FALSE, col.names = TRUE, na = "",
         sep = "\t");

     ## Now essentially load it back, but assign column headers
     mirnaobj <- loadmirnapath( mirnafile = "mirnaobj.txt",
         pvaluecol = "P-value", groupcol = "GROUP", 
         mirnacol = "miRNA Name", assayidcol = "ASSAYID" );

     ## Display summary information for the resulting object
     mirnaobj;

