arithscan                package:qtl                R Documentation

_A_r_i_t_h_m_e_t_i_c _O_p_e_r_a_t_o_r_s _f_o_r _s_c_a_n_o_n_e _a_n_d _s_c_a_n_t_w_o _r_e_s_u_l_t_s

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

     Add or subtract LOD scores in results from 'scanone' or 'scantwo'.

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

     scan1+scan2
     scan1-scan2

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

scan1, scan2: Genome scan results on the same set of chromosomes and
          markers, as output by 'scanone' or 'scantwo'.

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

     This is used to calculate the sum or difference of LOD scores of
     two genome scan results.  It is particularly useful for
     calculating the LOD scores for QTL-by-covariate interactions (see
     the example, below). Note that the degrees of freedom are also
     added or subtracted.

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

     The same type of data structure as the input objects, with LOD
     scores added or subtracted.

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

     Karl W Broman, kbroman@biostat.wisc.edu

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

     data(fake.bc)

     fake.bc <- calc.genoprob(fake.bc, step=2.5)

     # covariates
     ac <- pull.pheno(fake.bc, c("sex","age"))
     ic <- pull.pheno(fake.bc, "sex")

     # scan with additive but not the interactive covariate
     out.acovar <- scanone(fake.bc, addcovar=ac)

     # scan with interactive covariate
     out.icovar <- scanone(fake.bc, addcovar=ac, intcovar=ic)

     # plot the difference of with and without the interactive covariate
     #     This is a LOD score for a test of QTL x covariate interaction
     plot(out.icovar-out.acovar)

