polygenicQTL: Run rrBLUP polygenic inheritance on an R/qtl model

In jtlovell/qtlTools: Data Processing and Plotting in Association with R/qtl

Description

polygenicQTL Parses and pushes qtl model data int rrBLUP's mixed model genomic selection pipe. Outputs polygenic inheritance stats.

Usage

polygenicQTL(cross, formula = NULL, qtl = NULL, pheno.col = 1,
  covar = NULL, rrBLUP.method = "REML", verbose = TRUE, ...)

Arguments

cross	A qtl cross object containing conditional genotype probabilites calculated with stepwidth = "fixed".
formula	The formula for the qtl, names of columns in the covariate dataframe and altnames of the QTL need to match exactly, or will be ignored.
qtl	A QTL model, generated by makeqtl (etc.) .
pheno.col	Character or numeric vector of length 1, indicating the phenotype to be tested.
covar	the covariate specified in the model / formula. See fitqtl.
rrBLUP.method	should reml or ml be run?
verbose	Should a normal or binary model be fit?
...	additional arguments passed on to rrBLUP::mixed.solve

Details

See rrBLUP::mixed.solve and rrBLUP::kin.blup

Value

A dataframe with 3 columns:

• "Vg"The genetic variance attributable to the kinship (polygenic)

• "Ve"The amount of environmental (residual) varaince

• "polyH2"the proportion of Vtotal in Vg. Equivalent to the amount of heritability attributable to kinship (polygenic) variance following incoporpation of any fixed effects

Examples

## Not run: 
library(qtlTools)
library(rrBLUP)
data(fake.f2)
cross<-fake.f2
cross<-calc.genoprob(cross, step = 12, stepwidth = "fixed")
qtl<-makeqtl(cross, chr = 13, pos = 28, what = "prob")
formula = " ~ Q1 + Q1*sex + sex"
covar = data.frame(sex = pull.pheno(cross, pheno.col = "sex"))
polygenicQTL(cross = cross, pheno.col = 1)
polygenicQTL(cross = cross, covar = covar, formula = "~ sex", pheno.col = 1)
polygenicQTL(cross = cross, qtl = qtl, formula = "~ Q1", pheno.col = 1)
polygenicQTL(cross = cross, qtl = qtl,covar = covar, formula = "~ Q1 + Q1*sex + sex", pheno.col = 1)

## End(Not run)

jtlovell/qtlTools documentation built on May 20, 2019, 3:14 a.m.