qtlThreshold           package:MetaNetwork           R Documentation

_E_s_t_i_m_a_t_e _Q_T_L _s_i_g_n_i_f_i_c_a_n_c_e _t_h_r_e_s_h_o_l_d.

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

     Simulation test to estimate empirical threshold for QTL
     significance. The trait  values are simulated using the median
     number of noise, median mean and  standard deviation from the
     observed trait data under the null hypothesis of no QTL.  At each
     simulation test, the highest absolute -log_{10}(p) value is
     recorded.  The threshold is set at desired alpha level (i.e. take
     the -log_{10}(p) value at the alpha proportion position of the
     permutation set).

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

     qtlThreshold(genotypes, traits, spike, 
                  n.simulations = 1000, alpha = 0.05)

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

genotypes: matrix of genotypes for each marker (rownames) and
          individual (columnnames), as numeric values 1, 2 or NA when
          missing.
           See 'genotypes' example data. 

  traits: matrix of phenotypes for each trait (rownames) and individual
           (columnnames), as numeric or NA when missing.
           See 'traits' example data.

   spike: numeric cut-off value to separate absent (qualitative) from 
          available (quantitative) trait abundance. 

n.simulations: (optional) number of simulations. Default is 1000 times. 

   alpha: (optional) numeric alpha level for the threshold. Default is
          0.05. 

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

     Returns the -log_{10}(p) significance threshold value for QTLs.

_N_o_t_e:

     The individual columns of 'genotypes' and 'traits' must have the
     same order. The names of individuals should be consistent over
     'genotypes' and 'traits'.

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

     Jingyuan Fu <j.fu@rug.nl>,  Morris Swertz <m.a.swertz@rug.nl>, 
     Ritsert Jansen <r.c.jansen@rug.nl>

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

     Fu J, Swertz MA, Keurentjes JJB, Jansen RC. MetaNetwork: a
     computational tool for the  genetic study of metabolism. Nature
     Protocols (2007). 

     <URL: http://gbic.biol.rug.nl/supplementary/2007/MetaNetwork>

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

     ## load the example data provided with this package                          
     data(genotypes)
     data(traits)                                                       
                                                  
     ##OR: load your own data                     
     #genotypes  <- loadData("genotypes.csv")
     #traits     <- loadData("traits.csv")  
                                                  
     ##estimate qtl threshold for significance with low count of simulations (advised: 1000)
     qtlThres    <- qtlThreshold(genotypes, traits, 4, n.simulations = 10)

     ##show the threshold
     qtlThres

