vqtl: Genome Scans to Accommodate and Target Genetic and Non-Genetic Effects on Trait Variance
Version 1.0

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.

AuthorRobert Corty
Date of publication2016-03-07 01:01:40
MaintainerRobert Corty <rcorty@gmail.com>
LicenseGPL-3
Version1.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("vqtl")

Popular man pages

get.additive.coef.from.3.genoprobs: Compute Additive 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
scanonevar: Conduct a scanonevar.
scanonevar.to.p.values: Convert Scanonevar from LODs to Empirical p-values
summary.scanonevar: Summary of Peaks in Scanonevar
units: Get units of a scanonevar object
See all...

All man pages Function index File listing

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

Functions

get.additive.coef.from.2.genoprobs Man page Source code
get.additive.coef.from.3.genoprobs Man page Source code
get.dom.coef.from.3.genoprobs Man page Source code
get.genoprobs.by.marker.name Man page Source code
get.genotypes.by.marker.name Man page Source code
get.peaks.from.scanonevar Man page Source code
is.scanonevar Man page Source code
margin.plot Man page Source code
plot.scanonevar Man page Source code
predictive.plot Man page Source code
scan.via.dglm Man page Source code
scanonevar Man page Source code
scanonevar.perm Man page Source code
scanonevar.to.p.values Man page Source code
summary.scanonevar Man page Source code
units Man page Source code
validate.convert.scanonevar.to.p.values Man page Source code
validate.input.scanonevar Man page Source code

Files

tests
tests/test1.R
NAMESPACE
data
data/data.R
R
R/get.dom.coef.from.3.genoprobs.R
R/get.peaks.from.scanonevar.R
R/scan.via.dglm.R
R/margin.plot.R
R/convert.scanonevar.to.p.values.R
R/get.genotypes.by.marker.name.R
R/validate.input.scanonevar.R
R/summary.scanonevar.R
R/scanonevar.perm.R
R/predictive.plot.R
R/units.R
R/vqtl.R
R/is.scanonevar.R
R/scanonevar.R
R/get.additive.coef.from.2.genoprobs.R
R/get.additive.coef.from.3.genoprobs.R
R/validate.convert.scanonevar.to.p.values.R
R/plot.scanonevar.R
R/get.genoprobs.by.marker.name.R
MD5
DESCRIPTION
man
man/units.Rd
man/scanonevar.Rd
man/margin.plot.Rd
man/get.additive.coef.from.2.genoprobs.Rd
man/is.scanonevar.Rd
man/summary.scanonevar.Rd
man/get.dom.coef.from.3.genoprobs.Rd
man/get.additive.coef.from.3.genoprobs.Rd
man/scan.via.dglm.Rd
man/get.peaks.from.scanonevar.Rd
man/validate.convert.scanonevar.to.p.values.Rd
man/scanonevar.to.p.values.Rd
man/scanonevar.perm.Rd
man/validate.input.scanonevar.Rd
man/predictive.plot.Rd
man/plot.scanonevar.Rd
man/get.genotypes.by.marker.name.Rd
man/get.genoprobs.by.marker.name.Rd
vqtl documentation built on May 19, 2017, 10:30 p.m.

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