loadmirnapathways         package:miRNApath         R Documentation

_L_o_a_d _g_e_n_e _t_o _p_a_t_h_w_a_y _a_s_s_o_c_i_a_t_i_o_n_s _f_o_r _m_i_R_N_A_p_a_t_h

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

     This method loads associations between genes and the pathways to
     which they belong.

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

     loadmirnapathways(mirnaobj, pathwayfile, genecol="Entrez Gene ID",
     pathwaycol="PATHWAY", columns=c(), pathwayidcol=NA)

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

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

pathwayfile: The file containing the gene to pathway associations. 

 genecol: The name of the column header which contains the gene names
          associated with pathway data. 

pathwaycol: The name of the column header which contains the pathway
          names. 

 columns: The names of any additional columns in the file being read
          which should equate with the mirnapath object. 

pathwayidcol: The (optional) column header for IDs associated with the
          pathway names. 

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

     The data loaded is expected to have gene names which exactly match
     those gene names loaded by 'loadmirnatogene'.

_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', 'runEnrichment'

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

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

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

     ## Load the gene to pathway associations
     mirnaobj <- loadmirnapathways( mirnaobj = mirnaobj, 
         pathwayfile = "mirnaPathways.txt", 
         pathwaycol = "Pathway Name", genecol = "Entrez Gene ID");

     ## Display summary, noting the number of genes reported
     mirnaobj;

