CTL mapping examples

CTL mapping has been applied in several datasets we show here some basic analysis I performed on the data. I start off by doing basic QC on the provided dataset, followed by QTL and CTL mapping.

Metabolites in Arabidopsis thaliana

Show the analysis of the 63 metabolites analysed by Gary Churchill.
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Individuals:403Traits:63
Markers:69Chromosomes:5
Results: Quality Control
QC of the genetic map
Fig 1-0 - QC - The genetic map
QC of trait correlation
Fig 1-1 - QC - Trait correlations

Results: CTL, QTL
We first show the comparison between a QTL and a CTL heatmap
QTL / CTL comparison plot
Fig 1-2 - QTL / CTL comparison heatmap


Classical traits + metabolites in 4 seed conditions Arabidopsis thaliana

Show the analysis of the classical traits and metabolites based on data collected by Ronny Joosen.
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Individuals:???Traits:???
Markers:69Chromosomes:5
Results: Quality Control
QC of the genetic map
Fig 1-0 - QC - The genetic map
QC of trait correlation
Fig 1-1 - QC - Trait correlations

Results: CTL, QTL
We first show the comparison between a QTL and a CTL heatmap
QTL / CTL comparison plot
Fig 1-2 - QTL / CTL comparison heatmap


Gene expression in Saccharomyces cerevisiae

Show the analysis of 3000 gene expression probes of Rachel Brem.
Read more...
Individuals:???Traits:3000
Markers:???Chromosomes:???
Results: Quality Control
TODO
Results: CTL, QTL
TODO


Metabolites in Arabidopsis thaliana

Show the analysis of the 24 metabolites of Ying Fu.
Read more...
Individuals:162Traits:24
Markers:117Chromosomes:5
Results: Quality Control
TODO
Results: CTL, QTL
TODO


Download the examples

Datasets are distributed with the R package (available from CRAN), additionally you can download the datasets and scripts here:

Contributors

Contact for problems/questions/suggestions: Danny Arends (Danny.Arends at Gmail.com)
(c) 2011 - Groningen Bioinformatics Centre :
Danny Arends - www.dannyarends.nl, Pjotr Prins - www.thebird.nl, and Ritsert C. Jansen - www.rug.nl/gbic