qtlProfiles {MetaNetwork} | R Documentation |
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
.
data(qtlProfiles)
A matrix of QTL -log_{10}(p) values for 24 traits (rows) and 117 markers(columns).
Jingyuan Fu <j.fu@rug.nl>, Morris Swertz <m.a.swertz@rug.nl>, Ritsert Jansen <r.c.jansen@rug.nl>
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.
Fu J, Swertz MA, Keurentjes JJB, Jansen RC. MetaNetwork: a computational tool for the genetic study of metabolism. Nature Protocols (2007).
http://gbic.biol.rug.nl/supplementary/2007/MetaNetwork
Use qtlMapTwoPart
to generate qtlProfiles
.
Use MetaNetwork
for automated analysis of this data set as part a genetic analysis protocol on metabolites.