vbscan                  package:qtl                  R Documentation

_G_e_n_o_m_e _s_c_a_n _f_o_r _t_r_a_i_t _w_i_t_h _s_o_m_e _u_n_d_e_f_i_n_e_d _v_a_l_u_e_s

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

     Performs a genome scan by interval mapping for a quantitative
     phenotype for which some individuals' phenotype is undefined (for
     example, the size of a lesion, where some individuals have no
     lesion).  The undefined value must correspond to either the
     largest phenotype or the smallest phenotype.

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

     vbscan(cross, chr, pheno.col=1, upper=FALSE,
            maxit=1000, tol=1e-8)

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

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

     chr: Vector indicating the chromosomes for which LOD scores should
          be calculated.

pheno.col: Column number in the phenotype matrix which should be used
          as the phenotype.

   upper: If true, the "undefined" phenotype is the maximum observed
          phenotype; otherwise, it is the smallest observed phenotype.

   maxit: Maximum number of iterations in the EM algorithm; used only
          in interval mapping.

     tol: Tolerance value for determining convergence in the EM
          algorithm; used only in interval mapping.

_D_e_t_a_i_l_s:

     The function requires that multipoint genotype probabilities are
     first calculated using `calc.genoprob'.  

     Describe the model here.

     Individuals with missing phenotypes are dropped.

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

     A matrix of dimension [n.pos x (2*n.gen+6)].  The columns are 
     chromosome number, position (in cM; female cM for the 4-way
     cross), LOD(p,mu), LOD(p), LOD(mu), estimates of the ps, estimates
     of the mus,  and residual SD.

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

     Karl W Broman, kbroman@jhsph.edu 
     <URL:
     http://biosun01.biostat.jhsph.edu/~kbroman/software/qtl.html>

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

     Boyartchuk VL, Broman KW, Mosher RE, D'Orazio SEF, Starnbach MN,
     Dietrich WF (2001) Multigenic control of Listeria monocytogenes
     susceptibility in mice. Nature Genetics 27:259-260 

     Broman KW, Boyartchuk VL, Dietrich WF (2000) Mapping time-to-death
     quantitative trait loci in a mouse cross with high survival rates.
     Technical Report MS00-04, Department of Biostatistics, Johns
     Hopkins University, Baltimore, MD

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

     `plot.scanone', `summary.scanone', `vbscan.perm', `calc.genoprob',
     `scanone'

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

     data(listeria)
     listeria$pheno <- log10(listeria$pheno)
     listeria <- calc.genoprob(listeria,step=1,off.end=0,err=0)
     output <- vbscan(listeria,upper=TRUE)
     plot(output)

