subset.qb               package:qtlbim               R Documentation

_S_u_b_s_e_t_t_i_n_g _B_a_y_e_s_i_a_n _i_n_t_e_r_v_a_l _m_a_p_p_i_n_g _d_a_t_a

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

     Subset Bayesian interval mapping iterations on number of QTL
     and/or chromosome pattern of QTL, using exact match or inclusive
     subsetting.

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

     ## S3 method for class 'qb':
     subset(x, nqtl=1, pattern=NULL, exact=FALSE, chr,
       region, offset = TRUE, restrict.pair = TRUE, ...)

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

       x: object of class 'qb' 

    nqtl: subset on number of QTL

 pattern: subset on chromosome pattern of QTL

   exact: subset on exact pattern or number of QTL if true

     chr: subset of chromosomes to plot (numerical indices or
          chromosome names)

  region: list containing 'chr', and 'start' and 'end' positions, for
          regions to include

  offset: indicates that 'start' and 'end' are in cM position if
          'TRUE'; otherwise they are in distance from first marker

restrict.pair: Restrict 'chr' selection to epistatic pairs with both in
          selected subset.

     ...: additional arguments to 'subset'

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

     Subset to include only iterations with at least 'nqtl' number of
     QTL and at least the 'pattern' across chromosomes. 'pattern' is a
     vector of chromosome identices, with repeats for multiple linked
     QTL on a chromosome. If 'exact=FALSE', then all iterations with at
     least the given 'pattern' and 'nqtl' are included. 'nqtl' will be
     reset to 'length(pattern)' if it is smaller than this value. Note
     that 'pattern' should be number codes corresponding to those used
     in the 'x' object. At present, chromosome names are not allowed.
     Further subsets to only include QTL from these iterations that are
     on chromosomes 'chr'.

_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:

     'read.cross'

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

     ## Subset to chr 1,2, and to within 10 cM of QTL on chr 1,2.
     qbSubset <- subset(qbExample, chr = c(1,2),
       region = data.frame(chr = c(1,2), start = c(35,2), end = c(55,22)))

