geneListPie-package       package:geneListPie       R Documentation

_P_r_o_f_i_l_i_n_g _a _g_e_n_e _l_i_s_t _i_n_t_o _G_O_s_l_i_m _o_r _K_E_G_G _f_u_n_c_t_i_o_n _p_i_e

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

     'geneListPie' package is for mapping a gene list to function
     categories defined in GOSlim or Kegg. The results can be plotted
     as a pie chart to provide a quick view of the genes distribution
     of the gene list among the function categories. The gene list must
     contain a list of gene symbols. The package contains a set of
     pre-processed gene sets obtained from Gene Ontology and MSigDB
     including human, mouse, rat and yeast. To provide a high level
     concise view, only GO slim and kegg are provided. The gene sets
     are regulared updated. User can also use customized gene sets.
     User can use the R Pie() or Pie3D() function for plotting the pie
     chart. Users can also choose to output the gene function mapping
     results and use external software such as Excel(R) for ploting.

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


       Package:   geneListPie
       Type:      Package
       Version:   1.0
       Date:      2009-10-06
       License:   GPL-3
       LazyLoad:  yes

     load.genelist() to load a list of gene symbols from a text file. 
      load.genesets() to load customized gene sets from a file.
     Otherwise use pre-packaged gene sets including gene sets from
     Human, Mouse, Rat, and Yeast for Biological Processes, Molecular
     Functions, and Cellular Components. 

     goslim.human.all 
      goslim.human.BP 
      goslim.human.CC 
      goslim.human.MF 
      goslim.mouse.all 
      goslim.mouse.BP 
      goslim.mouse.CC 
      goslim.mouse.MF 
      goslim.rat.all 
      goslim.rat.BP 
      goslim.rat.CC 
      goslim.rat.MF 
      goslim.yeast.all 
      goslim.yeast.BP 
      goslim.yeast.CC 
      goslim.yeast.MF 
      kegg2.5.generic 

     geneListProfile() will then generates the results for plotting
     function distribution or pie.
      printGeneListProfile() can be used for generating mapping results
     in text format 

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

     Xutao Deng

     Maintainer: Xutao Deng <xutaodeng@gmail.com>

_R_e_f_e_r_e_n_c_e_s:

     Gene Ontology <URL: http://www.geneontology.org/> MSigDB <URL:
     http://www.broadinstitute.org/gsea/msigdb/>

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

     data(goslim.human.BP)
     glist<-c("ABCB7","ABCF1","ABHD2","ACAD9","ACIN1","AMOTL1","ANLN","ANXA4","APBA2","APBA3","BAI3","BCLAF1","BEST1")
     r<-geneListProfile(goslim.human.BP, glist, threshold=1)
     labels<-sub("_", "__", r$labels) #remove the GO id labels for display, optional
     labels<-sub(".*__", "", labels)
     pie(r$sizes,labels=labels, main="GO Slim Biological Process Mapping")

     ##prepare a gene list in a single column or row
     #glist<-load.genelist("genelist.txt", format="column")
     ##this is how to load a customize gene set in a file
     #gs<-load.genesets("customized-genesets.txt")
     #r<-geneListProfile(gs, glist, threshold=5)
     #library(plotrix)
     #pie3D(r$sizes,labels=r$labels, main="customized Mapping")
     #printGeneListProfile(r)

