qtlProfiles {MetaNetwork}R Documentation

Example qtl profiles

Description

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.

Usage

data(qtlProfiles)

Format

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

Author(s)

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

Source

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.

References

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

See Also

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


[Package MetaNetwork version 1.0-0 Index]