plotP                  package:SPIA                  R Documentation

_S_P_I_A _t_w_o-_w_a_y _e_v_i_d_e_n_c_e _p_l_o_t

_D_e_s_c_r_i_p_t_i_o_n:

     Plots each pathway as a point, using the over-representation
     p-value, pNDE, and perturbations accumulation p-value, pPERT, as
     coordinates.

_U_s_a_g_e:

     plotP(x,threshold=0.05)

_A_r_g_u_m_e_n_t_s:

       x: A data frame produced by 'spia' function.

threshold: A numerical value between 0 and 1 to be used as significance
          threshold in inferring pathway significance.

_D_e_t_a_i_l_s:

     In this plot each pathway is a point and the coordinates are the
     log of pNDE (using a hypergeometric model) and the p-value from
     perturbations, pPERT. The oblique lines in the plot show the
     significance  regions based on the combined evidence.

_V_a_l_u_e:

     This function does not return any value. It only generates a plot.

_A_u_t_h_o_r(_s):

     Adi Laurentiu Tarca <atarca@med.wayne.edu>, Purvesh Khatri, Sorin
     Draghici

_R_e_f_e_r_e_n_c_e_s:

     Adi L. Tarca, Sorin Draghici, Purvesh Khatri, et. al, A Signaling
     Pathway Impact Analysis for  Microarray Experiments, 2008,
     Bioinformatics, 2009, 25(1):75-82. 

_S_e_e _A_l_s_o:

     'spia'

_E_x_a_m_p_l_e_s:

     # Examples use colorectal cancer dataset
     data(colorectalcancer)

     # pathway analysis based on combined evidence of ORA and perturbations
     # use nB=2000 or larger for more accurate results
     res<-spia(de=DE_Colorectal, all=ALL_Colorectal, organism="hsa",nB=200,plots=FALSE,verbose=TRUE,beta=NULL)

     #Generate the evidence plot
     plotP(res,threshold=0.1)

