genotypes {MetaNetwork}R Documentation

Example genotype data

Description

Example matrix of genotypes for each marker (rownames) and 162 Arabidopsis thaliana individuals (columnnames), as numeric values 1, 2 or NA when missing:

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

X1 X3 X4 X5 X6
PVV4 1 1 2 1 2
AXR-1 1 1 2 1 2
HH.335C-Col 1 1 1 1 2
DF.162L/164C-Col 1 1 1 1 2
EC.480C 1 1 1 1 2

Usage

data(genotypes)

Format

117 markers by 162 samples (RILS).

Author(s)

Jingyuan Fu <j.fu@rug.nl>, Joost Keurentjes <Joost.Keurentjes@wur.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 MetaNetwork for automated analysis of this data set as part a genetic analysis protocol on metabolites. Use qtlMapTwoPart for the calculation of qtlProfiles form genotypes.


[Package MetaNetwork version 1.0-0 Index]