vqtl: Genome Scans to Accommodate and Target Genetic and Non-Genetic Effects on Trait Variance

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In recognition that there are many factors (genetic loci, macro-genetic factors such as sex, and environmental factors) that influence the environmental variation, the 'vqtl' package conducts genome scans that accommodate and target these factors. The main functions of this package, scanonevar() and scanonevar.perm() take as input a cross object from the popular 'qtl' package.

Author
Robert Corty
Date of publication
2016-03-07 01:01:40
Maintainer
Robert Corty <rcorty@gmail.com>
License
GPL-3
Version
1.0

View on CRAN

Man pages

get.additive.coef.from.2.genoprobs
Compute Additive Coefficient From Two Genotype Probabilities
get.additive.coef.from.3.genoprobs
Compute Additive Coefficient From Three Genotype...
get.dom.coef.from.3.genoprobs
Compute Dominance Deviation Coefficient From Three Genotype...
get.genoprobs.by.marker.name
Get Genotype Probabilities From a Cross Object By Marker (or...
get.genotypes.by.marker.name
Get Genotypes From a Cross Object By Marker Name
get.peaks.from.scanonevar
Get Local Maxima from Scanonevar
is.scanonevar
is.scanonevar
margin.plot
Plot Phenotype of interest Averaged (Marginalized) Across...
plot.scanonevar
plot.scanonevar
predictive.plot
Plot Predictive Interval for Categorical Genotype/Phenotype...
scanonevar
Conduct a scanonevar.
scanonevar.perm
Conduct Scanonevars on Permuted Genotype Data
scanonevar.to.p.values
Convert Scanonevar from LODs to Empirical p-values
scan.via.dglm
Conduct a Scanonevar Using the DGLM Function
summary.scanonevar
Summary of Peaks in Scanonevar
units
Get units of a scanonevar object
validate.convert.scanonevar.to.p.values
Check the Compatibility of the Scanonevar to be Converted...
validate.input.scanonevar
Validate the Input before Conducting a Scanonevar

Files in this package

vqtl
vqtl/tests
vqtl/tests/test1.R
vqtl/NAMESPACE
vqtl/data
vqtl/data/data.R
vqtl/R
vqtl/R/get.dom.coef.from.3.genoprobs.R
vqtl/R/get.peaks.from.scanonevar.R
vqtl/R/scan.via.dglm.R
vqtl/R/margin.plot.R
vqtl/R/convert.scanonevar.to.p.values.R
vqtl/R/get.genotypes.by.marker.name.R
vqtl/R/validate.input.scanonevar.R
vqtl/R/summary.scanonevar.R
vqtl/R/scanonevar.perm.R
vqtl/R/predictive.plot.R
vqtl/R/units.R
vqtl/R/vqtl.R
vqtl/R/is.scanonevar.R
vqtl/R/scanonevar.R
vqtl/R/get.additive.coef.from.2.genoprobs.R
vqtl/R/get.additive.coef.from.3.genoprobs.R
vqtl/R/validate.convert.scanonevar.to.p.values.R
vqtl/R/plot.scanonevar.R
vqtl/R/get.genoprobs.by.marker.name.R
vqtl/MD5
vqtl/DESCRIPTION
vqtl/man
vqtl/man/units.Rd
vqtl/man/scanonevar.Rd
vqtl/man/margin.plot.Rd
vqtl/man/get.additive.coef.from.2.genoprobs.Rd
vqtl/man/is.scanonevar.Rd
vqtl/man/summary.scanonevar.Rd
vqtl/man/get.dom.coef.from.3.genoprobs.Rd
vqtl/man/get.additive.coef.from.3.genoprobs.Rd
vqtl/man/scan.via.dglm.Rd
vqtl/man/get.peaks.from.scanonevar.Rd
vqtl/man/validate.convert.scanonevar.to.p.values.Rd
vqtl/man/scanonevar.to.p.values.Rd
vqtl/man/scanonevar.perm.Rd
vqtl/man/validate.input.scanonevar.Rd
vqtl/man/predictive.plot.Rd
vqtl/man/plot.scanonevar.Rd
vqtl/man/get.genotypes.by.marker.name.Rd
vqtl/man/get.genoprobs.by.marker.name.Rd