get_H2: 'Get Broad sense heritability from BLUP model.'

In jyanglab/g3tools: For Genomics, quantGen, and popGen studies, especially for crop species.

Description

Run the model fit using function "get_BLUP" and get H2.

Usage

get_H2(fit, numerator = "Line", denominator = data.frame(f = c("Line",
  "Line:Year", "Line:Loc", "Residual"), df = c(1, 2, 2, 4)))

Arguments

fit	Model fit returned from get_BLUP [model].
numerator	Numerator of Vg/Ve, [char].
denominator	Denominator of Vg/Ve [data.table], 2nd, degree of freedom. i.e. data.frame(f=c("Line", "Line:Year", "Line:Loc", "Residual"), df=c(1, 2, 2, 4))

Value

return A value of heritability.

Examples

pheno <-  read.csv("data/pheno.csv", header=T)
fit <- get_BLUP(data = df, model = Brix ~ (1|Line) + (1|Loc) + (1|Year) + (1|Line:Loc) + (1|Line:Year),
                 which.factor = "Line", outfile="data/blup.csv")
get_H2(fit, numerator="Line",
       denominator=data.frame(f=c("Line", "Line:Year", "Line:Loc", "Residual"),
       df=c(1, 2, 2, 4)))

jyanglab/g3tools documentation built on May 20, 2019, 6:27 a.m.