geneListProfile         package:geneListPie         R Documentation

_P_r_o_f_l_i_n_g _a _g_e_n_e _l_i_s_t _a_g_a_i_n_s_t _g_e_n_e _s_e_t_s

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

     number is the number of overlapping genes between the gene list
     and the gene set.

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

     geneListProfile(gs, glist, threshold = 10)

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

      gs: gene sets, use prepackaged or user loaded 

   glist: gene list loaded by user 

threshold: specify the mininum number of overlapping genes in a gene
          set to output. This is to avoid displaying gene sets with
          very few overlapping genes. For each gene set, if the number
          of overlapping genes is smaller than the threshold, the set
          of overlapping genes will be combined to a gene set labeled
          "Others" 

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

 labels : the labels of the gene sets

  sizes : the number of overlapping genes of gene sets against gene
          list

symbols : the gene symbols of overlapping genes

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

     Xutao Deng

_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")

