plotLodProfile              package:qtl              R Documentation

_P_l_o_t _1-_d _L_O_D _p_r_o_f_i_l_e_s _f_o_r _a _m_u_l_t_i_p_l_e _Q_T_L _m_o_d_e_l

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

     Use the results of 'refineqtl' to plot one-dimensional LOD
     profiles for each QTL.

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

     plotLodProfile(qtl, chr, incl.markers=TRUE, gap=25, lwd=2, lty=1, col="black",
                    qtl.labels=TRUE, mtick=c("line", "triangle"),
                    show.marker.names=FALSE, alternate.chrid=FALSE,
                    add=FALSE, ...)

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

     qtl: An object of class '"qtl"'; must have been produced by
          'refineqtl' using 'keeplodprofiles=TRUE'.

     chr: Optional vector indicating the chromosomes to plot. 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.

incl.markers: Indicate whether to plot line segments at the marker
          locations.

     gap: Gap separating chromosomes (in cM).

     lwd: Line widths for each QTL trace (length 1 or the number of
          QTL).

     lty: Line types for each QTL trace (length 1 or the number of
          QTL).

     col: Line col for each QTL trace (length 1 or the number of QTL).

qtl.labels: If TRUE, place a label on each QTL trace.

   mtick: Tick mark type for markers (line segments or upward-pointing
          triangels).

show.marker.names: If TRUE, show the marker names along the x axis.

alternate.chrid: If TRUE and more than one chromosome is plotted,
          alternate the placement of chromosome  axis labels, so that
          they may be more easily distinguished.

     add: If TRUE, add curves to a current plot.

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

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

     The function plots LOD profiles in the context of a multiple QTL
     model, using a scheme best described in Zeng et al. (2000).  The
     position of each QTL is varied, keeping all other loci fixed.  If
     a QTL is isolated on a chromosome, the entire chromosome is
     scanned; if there are additional linked QTL, the position of a QTL
     is scanned over the largest interval possible without allowing the
     order of QTLs along a chromosome to change.  At each position for
     the QTL being scanned, we calculate a LOD score comparing the full
     model, with the QTL of interest at that particular position (and
     all others at their fixed positions) to the model with the QTL of
     interest (and any interactions that include that QTL) omitted.  

     Care should be take regarding the arguments 'lwd', 'lty', and
     'col'; if vectors are given, they should be in the order of the
     QTL within the object, which may be different than the order in
     which they are plotted.  (The LOD profiles are sorted by
     chromosome and position.)

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

     None.

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

     Karl W Broman, kbroman@biostat.wisc.edu

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

     Zeng  Z.-B., Liu, J., Stam, L. F., Kao, C.-H., Mercer, J. M. and
     Laurie, C. C. (2000) Genetic architecture of a morphological shape
     difference between two Drosophila species. _Genetics_ *154*,
     299-310.

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

     'refineqtl', 'makeqtl', 'scanqtl'

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

     data(fake.bc)

     fake.bc <- calc.genoprob(fake.bc, step=2)
     qtl <- makeqtl(fake.bc, chr=c(2,5), pos=c(32.5, 17.5), what="prob")

     out <- scanone(fake.bc, method="hk")

     # refine QTL positions and keep LOD profiles
     rqtl <- refineqtl(fake.bc, qtl=qtl, method="hk", keeplodprofile=TRUE)

     # plot the LOD profiles
     plotLodProfile(rqtl)

     # add the initial scan results, for comparison
     plot(out, add=TRUE, chr=c(2,5), col="red")

