effectscan                package:qtl                R Documentation

_P_l_o_t _a_l_l_e_l_i_c _e_f_f_e_c_t _a_c_r_o_s_s _t_h_e _w_h_o_l_e _g_e_n_o_m_e

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

     This function is used to plot allelic effect at all markers for
     selected chromosomes. For backcross, there will be only one line
     represents the additive effect. For F2, there will be two lines
     represent additive and dominance effects.

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

     effectscan(cross, pheno.col=1, chr, ylim, gap=25,
                col=c("black","blue","red"), lty=c(1,2,3), lwd=2,
                mtick=c("line", "triangle"), main, add.legend=TRUE,
                ...)

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

   cross: An object of class 'cross'.

pheno.col: Column number in the phenotype matrix which to be drawn in
          the plot.

     chr: Chromosome number to be drawn in the plot.

    ylim: y-axis limit.

     gap: Gap separating chromosomes (in cM).

     col: Line colors.

     lty: Line types.

     lwd: Line widths.

   mtick: Tick mark type for markers.

    main: Figure title.

add.legend: A logical value to indicate add legend or not.

     ...: Passed to the function 'plot' when it is called.

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

     None.

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

     Hao Wu, hao@jax.org

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

     'effectplot', 'plot.pxg'

_E_x_a_m_p_l_e_s:

     data(fake.f2)
     # allelic effect on whole genome
     effectscan(fake.f2, ylim=c(-6,3))
     # on first 4 chromosomes, use triangle as marker ticks
     effectscan(fake.f2, chr=1:4, ylim=c(-6,3), mtick="triangle")

