qb.get                package:qtlbim                R Documentation

_I_n_t_e_r_n_a_l _q_t_l_b_i_m _r_o_u_t_i_n_e_s

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

     These are internal qtlbim routines that are made visible in the
     namespace for technical use.

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

     covar.mean(qbObject, adjust.covar, verbose = FALSE)
     pull.grid(qbObject, offset, spacing, mask.region)
     qb.cross(qbObject)
     qb.demo()
     qb.get(qbObject, element, sub)
     qb.load(cross, qbObject, dir, file)
     qb.save(cross, qbObject, dir, file)
     qb.reorder(qbObject)

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

qbObject: Object of class 'qb'.

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

 verbose: Verbose mode if 'TRUE'.

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

  offset: Offset by first marker if 'TRUE'.

 spacing: Add columns for 'map', 'eq.spacing' and 'xchr' if 'TRUE'.
          This corresponds to 'map' element of a 'scantwo' object.

mask.region: Subset genome regions if 'TRUE' (see 'subset.qb').

 element: Character string for element of 'qbObject' to get. Typically
          this is a parameter to 'qb.data', 'qb.model' or 'qb.mcmc', or
          it is one of the MCMC sample files in 'output.dir', from
          'c("iterdiag", "mainloci", "pairloci", "covariates",
          "gbye")'.

     sub: Character string for subelement of 'qbObject' to get.

     dir: Character string name of directory for load if 'qbObject'
          does not exist.

    file: Character string name of file for load if 'qbObject' does not
          exist.

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

     These are all internal routines. But some may be useful beyond.

     'qb.demo' is called in 'demo(qb.tour)' and provides an interactive
     selection of the 'R/qtlbim' demos.

     'qb.cross' extracts the 'cross' object associated with 'qbObject'.
     'qb.get' is the internal main routine for extracting information
     from a 'qbObject'. As stated elsewhere, currently 'qbObject'
     refers to objects that are critical to it but not part of it: the
     'cross' object used to create it and the MCMC samples in files in
     'output.dir'.

     'covar.mean' finds covariate means or adjusts them to
     user-supplied values.

     'pull.grid' pulls the grid of pseudomarkers from the 'cross'
     object associated with 'qbObject'. The option 'spacing' determines
     whether this is in a format similar to 'scanone' ('FALSE') or
     'scantwo' ('TRUE'). It is used 'qb.get' when accessing external
     MCMC sample files and by several other routines that require
     pseudomarker information, notably genotype probabilities.

     'qb.reorder' is called by 'qb.mcmc' to create pointers to reorder
     the MCMC samples so that chromosome numbers and positions within
     chromosomes are in increasing order. It creates the 'subset'
     element of a 'qb' object.

     'qb.save' and 'qb.load' are used to speed up examples and
     vignettes by saving and loading an external workspace containing a
     'cross' and a 'qb' object. 'qb.save' returns 'TRUE' if the save
     was successful. 'qb.load' returns 'TRUE' if the objects exist
     already or they were loaded properly.

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

     covar.mean(qbExample)
     qb.get(qbExample, "output.dir")
     summary(qb.cross(qbExample))
     temp <- qb.get(qbExample, "iterdiag")
     dim(temp)
     names(temp)

     ## Not run: 
     ## The following should have no effect.
     qbExample <- qb.reorder(qbExampleb
     ## End(Not run)

     ## You can call the following rather than demo() to get a tour.
     qb.demo()

