units
(Package: vqtl) :
Get units of a scanonevar object
Utility function to get the units of a scanonevar, which is either 'LODs' (logarithm of the odds between null and alternative model) or 'emp.ps' (empirically determined p.value of that LOD)
● Data Source:
CranContrib
● Keywords:
● Alias: units
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scanonevar
(Package: vqtl) :
Conduct a scanonevar.
scanonevar conducts a scanonevar, a genome scan that takes into account genetic and non-genetic effects on residual (environmental) variation in the trait of interest.
● Data Source:
CranContrib
● Keywords:
● Alias: scanonevar
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margin.plot
(Package: vqtl) :
Plot Phenotype of interest Averaged (Marginalized) Across Specified Markers and Phenotypes
margin.plot should be used to visually investigate the relationship between the phenotype of interest and other phenotypes. margin.plot can also be used to visualize the relationship between the phenotype of interest and genetic loci of interest, but predictive.plot is usually preferrable.
● Data Source:
CranContrib
● Keywords:
● Alias: margin.plot
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get.additive.coef.from.2.genoprobs should not typically be called by a user. It is used to reliably set up model coefficients from genotype probabilities.
● Data Source:
CranContrib
● Keywords:
● Alias: get.additive.coef.from.2.genoprobs
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Tests whether an object is a valid scanonevar object
● Data Source:
CranContrib
● Keywords:
● Alias: is.scanonevar
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summary.scanonevar
(Package: vqtl) :
Summary of Peaks in Scanonevar
summary.scanonevar prints out the loci in a scanonevar object that exceed thresh. It is an S3 generic for summary(). It handles scanonevar objects in both LOD units and empirical p value units.
● Data Source:
CranContrib
● Keywords:
● Alias: summary.scanonevar
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get.dom.coef.from.3.genoprobs
(Package: vqtl) :
Compute Dominance Deviation Coefficient From Three Genotype Probabilities
get.dom.coef.from.3.genoprobs should not typically be called by a user. It is used to reliably set up model coefficients from genotype probabilities.
● Data Source:
CranContrib
● Keywords:
● Alias: get.dom.coef.from.3.genoprobs
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get.add.coef.from.3.genoprobs should not typically be called by a user. It is used to reliably set up model coefficients from genotype probabilities.
● Data Source:
CranContrib
● Keywords:
● Alias: get.additive.coef.from.3.genoprobs
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scan.via.dglm
(Package: vqtl) :
Conduct a Scanonevar Using the DGLM Function
scan.via.dglm should not typically be called by a user. This function is used by both scanonevar and scanonevar.perm. This function is not typically necessary for a typical user.
● Data Source:
CranContrib
● Keywords:
● Alias: scan.via.dglm
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get.peaks.from.scanonevar scans the genome for loci such that the locus to the left has a lower value and the locus to the right has a lower value. This value can be either LOD score or -log10(p-value)
● Data Source:
CranContrib
● Keywords:
● Alias: get.peaks.from.scanonevar
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providing 
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