goTools               package:goTools               R Documentation

_W_r_a_p_p_e_r _f_u_n_c_t_i_o_n_s

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

     This functions will allow you to describe and compare sets of
     oligo ids using Gene Ontology database

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

     ontoCompare(genelist,probeType=c("GO","hgu133a"),
     goType="All", endnode, method=c("TGenes", "TIDS", "none"), plot=FALSE,
     ...) 

     ontoPlot(objM, beside=TRUE, las=2,legend.text=TRUE, ...)

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

genelist: list of list of valid probe ids.

  method: method used to evaluate the percentage of oligos for each
          end-node. 'TGenes' = for each end node, return the number of
          direct children found / total number of probe ids. (default).
          This includes oligos which do not have GO annotations. 'TIDS'
          = for each end node, return the number of direct children
          found / total number of GO ids describing the list. 'none' =
          for each end node, return the number of direct children
          found.

probeType: type of input given to the function.Valid probe types
          include GO ids and any probes ids for which a BioC annotation
          package providing a mapping to GO is available. ontoCompare
          is expecting valid probe ids.

  goType: help sort the data by type. If 'All' (default), all oligos
          are taken into account. 'BP' restricts information to
          Biological Process, 'CC' to Cellular Component, and 'MF' to
          Molecular Function.

    plot: logical: if 'TRUE', results are output as a graph.

 endnode: list of GO ids corresponding to end-nodes of interest.

    objM: results from ontoCompare.

     ...: extra layout parameters to be passed to ontoPlot.

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

     Returns the percentage of probes children of nodes contained in
     endnode. If 'plot' = TRUE, results are plotted as a pie chart or a
     bargraph.

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

     Yee Hwa (Jean) Yang, Agnes Paquet

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

     # Examples use the probeID dataset. For description type ?probeID.
     # Not run

     #library(GO.db)
     #data(probeID)
     #ontoCompare(affylist, probeType="hgu133a", plot=TRUE)
     #res <- ontoCompare(operonlist["L1"], probeType="operon", method="TIDS")
     #ontoPlot(res, cex=0.7)

