qb.scantwo              package:qtlbim              R Documentation

_G_e_n_o_m_e _S_c_a_n _f_o_r _P_a_i_r_s _o_f _L_o_c_i _I_n_v_o_l_v_e_d _i_n _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 pair loci from the
     'qb' object and returns a data frame (of class 'qb.scanone')
     containing information on environmental variance, explained
     variance components, epistatic and non-epistatic variance
     components.

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

     qb.scantwo(qbObject, epistasis = TRUE, scan, type,
       upper.scan = "epistasis", lower.scan = "full", covar,
       adjust.covar, chr, min.iter = 1, verbose = FALSE)

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

qbObject: An object of class 'qb'.

epistasis: If 'TRUE' information on epistasis is included in the return
          value.

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

    type: Vector of two scan types; default is "heritability" (see
          below).

upper.scan: Vector of diagnostics to scan for upper triangle (see
          below).

lower.scan: Vector of diagnostics to scan for lower triangle (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'.

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).

 verbose: Give verbose feedback if 'TRUE'.

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

     The 'scan' and 'type' are similar to those used in 'qb.scanone'.
     However, here 'scan' is a list and 'type' is a vector, each with
     elements "lower" and "upper". You can either specify 'scan' as a
     list, or profide 'upper.scan' and 'lower.scan' separately.

     The 'scan' defaults for types other than counts to 'list(upper =
     "epistasis", lower = "full")'; you can modify the list 'scan' or
     the separate options 'upper.scan' and 'lower.scan'. The string
     "epistasis" is short-hand for the epistatic effects, 'c("aa",
     "ad", "da", "dd")'. The string "full" is shorthand for the
     epistatics effects plus main effects, 'c("add", "dom")', plus any
     GxE terms.

     The 'type' defaults to 'c(upper = "LPD", lower = "LPD")'. See
     'qb.scanone' for the range of possible types. Mostly the 2-D
     version of 'type' provides marginal summaries for pairs of loci.
     However, for type '"nqtl"', the marginal summaries involving main
     effects (e.g. with 'scan' values '"full"' or '"main"' or '"add"'
     or '"dom"') show, for each pair of chromosomes, the average number
     of QTL at both chromosomes.

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

     Returns an object of class 'qb.scantwo' (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:

     'plot.qb.scanone'

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

     temp <- qb.scantwo(qbExample)
     summary(temp)
     plot(temp)

