qb.sliceone              package:qtlbim              R Documentation

_G_e_n_o_m_e _S_l_i_c_e _t_o _d_e_t_e_c_t _Q_T_L _f_o_r _P_h_e_n_o_t_y_p_i_c _T_r_a_i_t

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

     This method extracts iteration diagnostics and mainloci from the
     'qb' object and returns a data frame (of class 'qb.sliceone').
     Generic summary and plot can be used for display.

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

     qb.sliceone(qbObject, slice, epistasis = TRUE, scan, type, covar,
       adjust.covar, chr, sum.scan = "yes", min.iter = 1,
       aggregate = TRUE, verbose = FALSE)
     ## S3 method for class 'qb.sliceone':
     summary(object, chr, ...)
     ## S3 method for class 'qb.sliceone':
     print(x, ...)
     ## S3 method for class 'qb.sliceone':
     plot(x, ..., scan, auto.par = TRUE)

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

qbObject: An object of class 'qb'.

  object: Object of class 'qb.sliceone'.

       x: Object of class 'qb.sliceone'.

   slice: Chromosomes to slice upon.

epistasis: If 'TRUE' then information about epistasis is included.

    scan: Vector of diagnostics to scan (see below).

    type: Type of scan; default is "heritability" (see below).

   covar: Covariate(s) to include; default is 'seq(nfixcov)' where
          'nfixcov' is taken from 'qb.data'. Set to 0 to exclude any
          covariates.

adjust.covar: Adjustments to covariates. Default is 'NA', which adjusts
          by covariate mean values. Values are assumed to be in order
          of fixed covariates.

     chr: Chromosomes to subset on if not 'NULL'.

sum.scan: Sum over 'scan' diagnostics if "yes" or "only"; only report
          'sum' if "only".

min.iter: Include only samples at loci if minimum number of iterations
          is at least 'min.iter'; default is to include all ('min.iter'
          = 1).

aggregate: Aggregate effects into main, epis, gbye if 'TRUE'.

 verbose: Give verbose feedback if 'TRUE'.

auto.par: Automatic setting of plot parameters for multiple plots if
          'TRUE'.

     ...: Arguments to be passed along.

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

     All arguments except 'slice' agree with 'qb.scanone'. The slice
     specifies a chromosome upon which to slice, yielding a 1-D scan of
     what might be seen on a 2-D scan using 'qb.scantwo'. One advantage
     of 'qb.sliceone' is that you can get 2-QTL cell means for the
     slice chromosome and the scanned chromosomes.

     The summary invokes 'summary.qb.scanone' to summarize slice by
     chromosome. The plot will by default give separate plots for each
     slice genotype and use 'plot.qb.scanone' to scan the chromosomes.
     If 'scan' is specified for 'plot.qb.sliceone', then those elements
     will be plotted. For instance, 'plot(x,scan="slice")' will plot
     the running average locus on the slice chromosome with respect to
     the other chromosomes.

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

     'qb.sliceone' returns an object of class 'qb.sliceone' (a data
     frame) containing effects selected according to 'type' and 'scan'.

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

     Brian S. Yandell, yandell@stat.wisc.edu

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

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

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

     'summary.qb.scanone', 'plot.qb.scanone'

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

     ## Get profile of heritability.
     temp <- qb.sliceone(qbExample, slice = 1, chr = 2:3)
     summary(temp)
     plot(temp)

     ## Get profile of cell means.
     temp <- qb.sliceone(qbExample, slice = 1, chr = 2:3, type = "cellmean")
     summary(temp)
     plot(temp)

