plotWhiskers              package:puma              R Documentation

_S_t_a_n_d_a_r_d _e_r_r_o_r_s _w_h_i_s_k_e_r_s _p_l_o_t

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

     A plot showing error bars for genes of interest.

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

     plotWhiskers(
             eset
     ,       comparisons=c(1,2)
     ,       sortMethod = c("logRatio", "PPLR")
     ,       numGenes=50
     ,       xlim
     ,       main = "PUMA Whiskers plot"
     ,       highlightedGenes=NULL
     )

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

    eset: An object of class 'ExpressionSet'. 

comparisons: A 2-element integer vector specifying the columns of data
          to be compared. 

sortMethod: The method used to sort the genes. "logRatio" is fold
          change. PPLR is Probability of Positive Log Ratio (as
          determined by the 'pumaDE' method). 

numGenes: Integer. Number of probesets to plot. 

    xlim: The x limits of the plot. See 'plot.default'. 

    main: A main title for the plot. See 'plot.default'. 

highlightedGenes: Row numbers of probesets to highlight with an
          asterisk. 

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

     This function has no return value. The output is the plot created.

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

     Richard D. Pearson

_S_e_e _A_l_s_o:

     Related method 'pumaDE'

