qtlSupportInterval        package:MetaNetwork        R Documentation

_E_s_t_i_m_a_t_e _Q_T_L _s_u_p_p_o_r_t _i_n_t_e_r_v_a_l

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

     For one QTL profile, significant QTLs are selected based on
     'qtlThres'.  The regions within the 'interval.dropoff' of these
     QTL peaks are defined as a support interval. The most left and the
     most right marker within each support interval are returned as
     matrix.

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

     qtlSupportInterval(markers, oneQtlProfile, qtlThres, interval.dropoff = 1.5)

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

 markers: matrix of markers (rownames) and their chromosome numbers 
          (column 1) and centi-Morgan positions (cM, column 2), ordered
          by position.
           See 'markers' example data.

oneQtlProfile: one row from the 'qtlProfiles' matrix of QTL mapping of
          traits (rownames)  to markers (columnnames), as -log_{10}(p)
          values.
           See 'qtlProfiles' example data.

qtlThres: numeric -log_{10}(p) threshold value for significant QTLs. 

interval.dropoff: numeric drop-off -log_{10}(p) value from the QTL peak
          that  defines left and right border of support interval
          (optional). Default is 1.5. 

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

     Returns a matrix of the markers number that define the left and
     right borders of each support interval for 'oneQtlProfile'.

_N_o_t_e:

     The markers should be ordered sequentially. The names of markers
     should be  consistent over 'markers' and 'qtlProfiles'.

_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>

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

     Use 'markers' as example data set or use 'loadData'  to load your
     own data.
      Use 'qtlMapTwoPart' for the calculation of 'qtlProfiles'.
       Use 'qtlThreshold' for the estimation of 'qtlThres' QTL 
     significance threshold.
      Use 'qtlSummary' for automated application of this function to 
     produce a support interval summary for a set 'qtlProfiles'.
      Use 'MetaNetwork' for automated appliction of this function as 
     part a genetic analysis protocol on metabolites.

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

     ## load the example data provided with this package                          
     data(markers)   
     data(genotypes)
     data(traits)                                                       
                                                  
     ##OR: load your own data                     
     #markers    <- loadData("markers.csv")
     #genotypes  <- loadData("genotypes.csv")
     #traits     <- loadData("traits.csv")  
                                                  
     ##calculate the two part qtl for only the first trait
     qtlProfiles <- qtlMapTwoPart(genotypes=genotypes, traits=traits[1,], spike=4)

     ##set the qtl threshold
     qtlThres    <- 3.79

     ##OR: estimate the threshold yourself
     #qtlThres   <- qtlThreshold(genotypes, traits, spike=4)

     ##calculate qtl confidence interval for the first qtl profile
     qtlSuppInt  <- qtlSupportInterval(markers, qtlProfiles[1,], qtlThres=qtlThres, 
                                       interval.dropoff = 1.5)    
                                       
     ##show the interval
     qtlSuppInt                                                             

