ctl (version 1.0.0-2)

QTLmapping: QTLmapping - QTL mapping method for CTL analysis

Description

Internal QTL mapping method used by the CTL analysis, associates every column in the genotypes with a single phenotype

Usage

QTLmapping(genotypes, phenotypes, phenocol = 1, verbose = TRUE)

Arguments

genotypes

Matrix of genotypes. (individuals x markers)

phenotypes

Matrix of phenotypes. (individuals x phenotypes)

phenocol

Which phenotype column(s) should we analyse. Default: Analyse a single phenotype.

verbose

Be verbose.

Value

vector of LOD scores for each genotype column, for phenotype column phenocol

Details

TODO

• NOTE: Slow approach, it is adviced to use your own QTL mapping data

References

TODO

See Also

• CTLscan - Main function to scan for CTL

• CTLscan.cross - Use an R/qtl cross object with CTLscan

• CTLsignificant - Significant interactions from a CTLscan

• plot.CTLscan - Plot the CTL curve for a single trait

Examples

# NOT RUN {
  library(ctl)
  data(ath.metabolites) # Arabidopsis Thaliana dataset
  qtldata <- QTLmapping(ath.metab$genotypes, ath.metab$phenotypes, phenocol = 23)
  plot(qtldata)         # Plot the results of the QTL scan for the phenotype
# }