qb.remove               package:qtlbim               R Documentation

_R_e_m_o_v_e _o_r _r_e_c_o_v_e_r _q_b _o_b_j_e_c_t _a_n_d _a_s_s_o_c_i_a_t_e_d _M_C_M_C _s_a_m_p_l_e_s

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

     This removes the object and the directory that contains the MCMC
     samples. It is not enough to remove the R object.

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

     qb.remove(qbObject, verbose = TRUE)
     qb.recover(cross, traitName, output.dir, n.thin = 40, n.burnin,
       algorithm = "M-H", genoupdate = FALSE, ...)

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

qbObject: Object of class 'qb' (see 'qb.mcmc').

 verbose: Print warning if 'TRUE'.

   cross: Object of class 'cross' (see 'read.cross').

traitName: Character string name of trait to recover.

output.dir: Character string with name of output directory (inferred if
          missing).

  n.thin: Thining of MCMC chain used in 'qb.mcmc'.

n.burnin: Burnin of MCMC chain used in 'qb.mcmc'.

algorithm: Algorithm of MCMC chain used in 'qb.mcmc'.

genoupdate: Genotype update flag for MCMC chain used in 'qb.mcmc'.

     ...: Options passed to 'qb.data' and 'qb.model'.

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

     At the present time, 'qb.mcmc' stores MCMC samples in external
     files located in directory 'output.dir', whose name is typically
     the 'traitName' followed by the date. 'qb.remove' removes this
     directory along with the 'qbObject'. 'qb.recover' attempts to
     recover the use of an orphaned 'output.dir' after a crash of R.
     These are fragile routines.

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

     Brian S. Yandell

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

     http://www.qtlbim.org

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

     'qb.mcmc', 'qb.genoprob'

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

     ## Not run: 
     ## Recover qbExample for trait "bp" of cross "hyper" using default output.dir.
     qbExample <- qb.recover(hyper, "bp")

     ## Remove internal qbExample and external output.dir.
     qb.remove(qbExample)
     ## End(Not run)

