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 (actually, an object of class '"scanone"', so that
     one may use 'plot.scanone', 'summary.scanone', etc.) 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.

     The row names indicate 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)

