makeqtl                 package:qtl                 R Documentation

_M_a_k_e _a _q_t_l _o_b_j_e_c_t

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

     This function takes a cross object and specified chromosome
     numbers and positions and pulls out the genotype probabilities or
     imputed genotypes at the nearest pseudomarkers, for later use by
     the function 'fitqtl'.

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

     makeqtl(cross, chr, pos, qtl.name, what=c("draws","prob"))

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

   cross: An object of class 'cross'. See 'read.cross' for details.

     chr: Vector indicating the chromosome for each QTL. (These should
          be character strings referring to the chromosomes by name.)

     pos: Vector (of same length as 'chr') indicating the positions on
          the chromosome to be taken. If there is no marker or
          pseudomarker at a position, the nearest position is used.

qtl.name: Optional user-specified name for each QTL, used in the
          drop-one-term ANOVA table in 'fitqtl'. If unspecified, the
          names will be of the form '"Chr1@10"' for a QTL on Chromsome
          1 at 10 cM.

    what: Indicates whether to pull out the imputed genotypes or the
          genotype probabilities.

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

     This function will take out the genotype probabilities and imputed
     genotypes if they are present in the input 'cross' object. If both
     fields are missing in the input object, the function will report
     an error. Before running this function, the user must have first
     run either 'sim.geno' (for 'what="draws"') or 'calc.genoprob' (for
     'what="prob"').

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

     An object of class 'qtl' with the following elements (though only
     one of 'geno' and 'prob' will be included, according to whether
     'what' is given as '"draws"' or '"prob"'): 

  'geno': Imputed genotypes.

  'prob': Genotype probabilities.

  'name': User-defined name for each QTL, or a name of the form
          '"Chr1@10"'.

'altname': QTL names of the form '"Q1"', '"Q2"', etc.

   'chr': Input vector of chromosome numbers.

   'pos': Input vector of chromosome positions.

 'n.qtl': Number of QTLs.

 'n.ind': Number of individuals.

 'n.gen': A vector indicating the number of genotypes for each QTL.

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

     Hao Wu; Karl W Broman, kbroman@biostat.wisc.edu

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

     'fitqtl', 'calc.genoprob', 'sim.geno', 'dropfromqtl',
     'replaceqtl', 'addtoqtl', 'summary.qtl', 'reorderqtl'

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

     data(fake.f2)

     # take out several QTLs and make QTL object
     qc <- c("1", "6", "13")
     qp <- c(25.8, 33.6, 18.63)
     fake.f2 <- subset(fake.f2, chr=qc)

     fake.f2 <- sim.geno(fake.f2, n.draws=8, step=2, err=0.001)
     qtl <- makeqtl(fake.f2, qc, qp, what="draws")
     summary(qtl)

