replaceqtl                package:qtl                R Documentation

_R_e_p_l_a_c_e _a _Q_T_L _i_n _a _q_t_l _o_b_j_e_c_t _w_i_t_h _a _d_i_f_f_e_r_e_n_t _p_o_s_i_t_i_o_n.

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

     This function replaces a QTL or QTLs in a qtl object with a
     different position.

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

     replaceqtl(cross, qtl, index, chr, pos, qtl.name, drop.lod.profile=TRUE)

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

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

     qtl: A qtl object, as created by 'makeqtl'.

   index: Numeric index indicating the QTL to be replaced.

     chr: Vector (of same length as 'index') indicating the chromosomes
          for the new QTL.

     pos: Vector (of same length as 'index') indicating the positions
          for the new QTL. If there is no marker or pseudomarker at a
          position, the nearest position is used.

qtl.name: Optional vector (of same length as 'index') of user-specified
          names for each new 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.

drop.lod.profile: If TRUE, remove any LOD profiles from the object.

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

     The input 'qtl' object, but with some QTL replaced by new ones. 
     See 'makeqtl' for details on the format.

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

     Karl W Broman, kbroman@biostat.wisc.edu

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

     'makeqtl', 'fitqtl', 'dropfromqtl', 'addtoqtl', '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 <- calc.genoprob(fake.f2, step=2, err=0.001)
     qtl <- makeqtl(fake.f2, qc, qp, what="prob")

     qtl <- replaceqtl(fake.f2, qtl, 2, 6, 48.1)

