tryallpositions             package:qtl             R Documentation

_T_e_s_t _a_l_l _p_o_s_s_i_b_l_e _p_o_s_i_t_i_o_n_s _f_o_r _a _m_a_r_k_e_r

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

     Try all possible positions for a marker, keeping all other markers
     fixed, and evaluate the log likelihood and estimate the chromosome
     length.

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

     tryallpositions(cross, marker, chr, error.prob=0.0001,
                     map.function=c("haldane","kosambi","c-f","morgan"),
                     m=0, p=0, maxit=4000, tol=1e-6, sex.sp=TRUE,
                     verbose=TRUE)

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

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

  marker: Character string with name of the marker to move about.

     chr: A vector specifying which chromosomes to test for the
          position of the marker.    This should be a vector of
          character strings referring to chromosomes by name; numeric
          values are converted to strings.  Refer to chromosomes with a
          preceding '-' to have all chromosomes but those considered. 
          A logical (TRUE/FALSE) vector may also be used.

error.prob: Assumed genotyping error rate used in the calculation of
          the penetrance Pr(observed genotype | true genotype).

map.function: Indicates whether to use the Haldane, Kosambi,
          Carter-Falconer, or Morgan map function when converting
          genetic distances into recombination fractions. (Ignored if m
          > 0.)

       m: Interference parameter for the chi-square model for
          interference; a non-negative integer, with m=0 corresponding
          to no interference. This may be used only for a backcross or
          intercross.

       p: Proportion of chiasmata from the NI mechanism, in the Stahl
          model; p=0 gives a pure chi-square model.  This may be used
          only for a backcross or intercross.

   maxit: Maximum number of EM iterations to perform.

     tol: Tolerance for determining convergence.

  sex.sp: Indicates whether to estimate sex-specific maps; this is 
          used only for the 4-way cross.

 verbose: If TRUE, print information on progress.

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

     A data.frame with each row being a possible position for the
     marker. The first two columns are the chromosome ID and position. 
     The third column is a LOD score comparing the hypotheses that the
     marker in that position versus the hypothesis that it is not
     linked to that chromosome.

     In the case of a 4-way cross, with 'sex.sp=TRUE', there are two
     additional columns with the estimated female and male genetic
     lengths of the respective chromosome, when the marker is in that
     position. With 'sex.sp=FALSE', or for other types of crosses,
     there is one additional column, with the estimated genetic length
     of the respective chromosome, when the marker is in that position.

     A final column contains a character string indicating the nearest
     flanking markers for each interval.

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

     Karl W Broman, kbroman@biostat.wisc.edu

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

     'est.map', 'ripple', 'est.rf', 'switch.order', 'movemarker'

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

     data(fake.bc)
     tryallpositions(fake.bc, "D7M301", 7, error.prob=0, verbose=FALSE)

