CTLscan.cross | R Documentation |
Scan for Correlated Trait Locus (CTL) in populations (using an R/qtl cross object)
CTLscan.cross(cross, ...)
cross |
An object of class |
... |
Passed to
|
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NOTE: Main bottleneck of the algorithm is the RAM available to the system
CTLscan object, a list with at each index a CTL matrix (Rows: Phenotypes, Columns: Genetic markers) for the phenotype.
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Danny Arends Danny.Arends@gmail.com
Maintainer: Danny Arends Danny.Arends@gmail.com
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CTLscan
- Main function to scan for CTL
CTLsignificant
- Significant interactions from a CTLscan
CTLnetwork
- Create a CTL network from a CTLscan
image.CTLobject
- Heatmap overview of a CTLscan
plot.CTLscan
- Plot the CTL curve for a single trait
library(ctl)
data(multitrait) # Arabidopsis Thaliana (R/qtl cross object)
mtrait <- calc.genoprob(multitrait) # Calculate genotype probabilities
qtls <- scanone(mtrait, pheno.col = 1) # Scan for QTLS using R/qtl
ctls <- CTLscan.cross(mtrait, phenocol = 1, qtl = FALSE)
ctls[[1]]$qtl <- qtls[,3]
ctl.lineplot(ctls, qtls[,1:2], significance = 0.05) # Line plot all the phenotypes
summary <- CTLsignificant(ctls) # Get a list of significant CTLs
summary
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