masterSnps              package:GGtools              R Documentation

_v_i_s_u_a_l_i_z_e _a _m_u_l_t_i_G_w_S_n_p_S_c_r_e_e_n_R_e_s_u_l_t

_D_e_s_c_r_i_p_t_i_o_n:

     visualize a multiGwSnpScreenResult

_U_s_a_g_e:

     masterSnps(mgw, n = 50, auto = TRUE, orgdb = "org.Hs.eg.db", minl10 = 5, 
     gstart = 0, gend = 3e+09,
     genomesize = 3e+09, pcex = 1, pal = rainbow(20), numxax=FALSE, ...)

_A_r_g_u_m_e_n_t_s:

     mgw: a multiGwSnpScreenResult, for example from gwSnpTests with a
          GeneSet on lhs of formula 

       n: number of best snps to retain per gene

    auto: restrict attention to autosomes? 

   orgdb: an annotation library like org.Hs.eg.db 

  minl10: threshold of -log10 p above which we keep SNP for plotting

  gstart: position at which genome-wide SNP locations begin

    gend: position at which genome-wide SNP locations end

genomesize: number of bases over which plotting will be conducted
          (e.g., ylim=c(0, genomesize) ) 

    pcex: cex setting for pch of plot 

     pal: a palette to differentiate gene coloring 

  numxax: logical: if TRUE, x axis labels genomic coordinates,
          otherwise chromosome 

     ...: args passed to plot() 

_D_e_t_a_i_l_s:

     experimental display with snp location as ordinate and gene
     location as abscissa - point plotted if snp is associated with
     gene at p smaller than the threshold specified

_V_a_l_u_e:

     a list with self-describing elements

_A_u_t_h_o_r(_s):

     VJ Carey <stvjc@channing.harvard.edu>

_E_x_a_m_p_l_e_s:

     if (require("GGdata")) {
      data(fheadFits)
      mm7 = masterSnps(fheadFits, minl10=7, pal=rainbow(10))
      }

