qb.genoprob              package:qtlbim              R Documentation

_G_r_i_d _p_o_i_n_t _a_n_d _g_e_n_o_t_y_p_e _p_r_o_b_a_b_i_l_i_t_y _c_o_m_p_u_t_a_t_i_o_n _m_e_t_h_o_d

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

     This function is used to compute putative QTL positions and
     genotypic probabilities at these positions. The genotypic
     probabilities for missing marker genotypes are also computed.

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

     qb.genoprob(cross, map.func = c("Haldane","Kosambi"), step = 2,
       tolerance = 1e-6, ...)

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

   cross: An object of class 'cross'. See 'read.cross' for details.

map.func: Indicates whether to use the "Haldane" or "Kosambi" map
          function when converting genetic distances to recombination
          fractions.

    step: Distance (in cM) between positions at which putative QTL
          positions and their genotype probabilities are calculated.
          However, specifying 'step = 0' would assume marker positions
          as putative QTL locations and genotypic probabilities would
          be calculated only for markers with missing genotype.

tolerance: Minimum separation of markers enforced by 'jittermap'.

     ...: Extra arguments to pass to 'calc.genoprob'.

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

     'qb.genoprob' first ensures marker separation is at least
     'tolerance', and then computes genotype probabilities at
     pseudomarkers spaced approximately 'step' units apart using
     'calc.genoprob'. See 'calc.genoprob' for value.

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

     Dr. Nengjun Yi, et al.,  nyi@ms.ssg.uab.edu

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://www.qtlbim.org>

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

     'jittermap', 'calc.genoprob'.

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

     ## calculate grids and genotypic probabilites
     cross <- qb.genoprob(cross,map.func="Haldane",step=2)

