QTLRel Package: functionalities (3)

17. nullSim: Simulate null distribution

Simulate distribution under the hypothesis of no QTL by permutation (of genotypic data) or gene dropping.

Two methods considered here are permutation test and gene dropping test as described as follows.

Permutation test. Depending on the genome-scan, one can provide either gdat or prdat respectively corresponding to single-marker analysis or interval mapping. Then only arguments in scanOne are needed in addition to method and ntimes.

Gene dropping test. If prdat is provided, then gdat will be ignored. The procedure will first call genoSim to generate new genotype data and then call genoProb to generate data for Haley-Knott interval mapping. If prdat is not provided, then gdat should be provided. The procedure will generate new genotype data and scan the genome using these generated genotype data. Haldane mapping function is used to generate data.

18. pedRecode: Recode a Pedigree, Prepare a pedigree in a format that is suitable for certain functions

19. plotit: Plot mapping results.

20. qqPlot: Quantile-Quantile Plots with the ability to draw confidence bands.

21. qtl2rel: Canvert data from R/qtl to QTLRel format, Covnert the data for a QTL mapping experiment from the R/qtl format to that used by QTLRel.

The input cross must by an intercross (class "f2")

Simple pedigree information is created, assuming that data are from a standard intercross.

22. qtlVar: QTL Variance, Estimate variance in a quantitative trait induced by QTL.

23. rel2qtl: Convert data from QTLRel to R/qtl format.

Pedigree information is ignored, and X chromosome data is omitted.

The data are treated as an intercross.

24. rem: Random effect matrices, Construct matrices associated with random effects.

25. scanOne: Genome Scan for QTL, Evaluate log-likelihood ratio test statistics or P-values at scanning loci along the genome.

The test at a scanning locus under assumption of no QTL effect versus the assumption of QTL effect is performed by conditioning on the estimated polygenic variance-covariance matrix. Normality is assumed for the random effects.

It is possible to extend the Haley-Knott approach to multiple-allelic cases under the assumption that allele effects are all additive. Then, prdat should be provided and be of class "addEff".

26. scanTwo: Genome Scan for Epistasis, Evaluate log-likelihood ratio test statistic for epistasis (QTL by QTL interaction)