qtlProfiles           package:MetaNetwork           R Documentation

_E_x_a_m_p_l_e _q_t_l _p_r_o_f_i_l_e_s

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

     Example matrix of QTL mapping profiles of traits (rownames)  on to
     markers (columnnames), calculated from Arabidopsis thaliana
     'genotypes' and 'traits' example datasets,  as -log_{10}(p)
     values. The +/- sign indicates the direction of the additive
     effect:                     values are positive if the QTL has
     higher metabolite abundance for individuals        carrying the
     genotype 2 than those carrying the genotype 1; values are negative
      otherwise.


     >data(qtlProfiles)
     >qtlProfiles[1:5,1:5]

                                    PVV4        AXR-1  HH.335C-Col  DF.162L/164C-Col     EC.480C
       3-Hydroxypropyl         1.1003510   1.52622550    0.7823755        0.69234969   1.0440796
       4-Hydroxybutyl          0.3007378   1.86596872    2.3859329        2.24693677   1.7367161
       4-Methylsulfinylbutyl  -0.1738533   0.08042058    0.1171418        0.02829792  -0.1050181
       3-Butenyl              -0.1875411  -1.16887454   -0.8904340       -0.80973239  -0.9517352
       3-Methylthiopropyl      0.5516505   0.33930888    0.3652804        0.36563859   0.2445772

     This matrix can be produced by functions 'qtlMapTwoPart' or
     'MetaNetwork'.

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

     data(qtlProfiles)

_F_o_r_m_a_t:

     A matrix of QTL -log_{10}(p) values for 24 traits (rows) and 117
     markers(columns).

_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>

_S_o_u_r_c_e:

     Keurentjes JJB, FU J, de vos CHR, Lommen A, Hall RD, Bino RJ, van
     der Plas LHW, Jansen RC, Vreugdenhil D and Koornneef M. The
     genetics of plant metabolism. Nature Genetics (2006) 7: 842-849.

_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 'qtlMapTwoPart' to generate 'qtlProfiles'.
      Use 'MetaNetwork' for automated analysis of this data set as part
     a genetic analysis protocol on metabolites.

