GWplot                 package:GWAF                 R Documentation

_f_u_n_c_t_i_o_n _f_o_r _m_a_k_i_n_g _g_e_n_o_m_e-_w_i_d_e _p-_v_a_l_u_e _p_l_o_t

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

     GWplot function plots -log_{10} p-value based on SNP's chromosomal
     position in bitmap format.

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

     GWplot(data, pval, pos, chr, chr.plot = c(1:22, "X"), title.text = "", ylim = Inf, outfile, cutoff1 = 5e-08, cutoff2 = 4e-07)

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

    data: a dataframe that contains p-values, chromosome number and
          physical position of SNPs 

    pval: a character string correspong to the name of the p-value
          column 

     pos: a character string correspong to the name of column with SNP
          physical positions  

     chr: a character string correspong to the name of column with SNP
          chromosome number 

chr.plot: the chsomosomes of interest for GWplot; either 1:22 or
          c(1:22,"X"), default chr.plot=c(1:22,"X"), "X" for X
          chromosome 

title.text: the title of the genome-wide p-value plot 

    ylim: the maximum of -log_{10} p-value to be plotted, useful when
          not want to plot extremely small p-values 

 outfile: the file name (xxxx.bmp) for output plot in bitmap format 

 cutoff1: genome-wide significance; default is 5E-8 ; p-values below
          this threshold will be highlighted in red

 cutoff2: suggestive genome-wide significance; default is 4E-7;
          p-values below this threshold but above cutoff1 will be
          highlighted in blue 

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

     When the dataset has 0 p-value, GWplot will generate pvalzero.csv
     that contain the results with 0 p-value and make the genome-wide
     p-value plot by replacing 0 p-value with 5E-324. P-values that
     reach genome-wide significance are displayed in red color;
     P-values that reach  suggestive genome-wide significance but not
     genome-wide significance are displayed in blue color.

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

     Qiong Yang <qyang@bu.edu> and Ming-Huei Chen <mhchen@bu.edu>

