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Test Syntax

Published Date

Input files

We will simulate a phenotype and prepare all input files except the array of haplotype probabilities.

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animals <- rownames(model.probs)
markers <- dimnames(model.probs)[[3]]
n <- nrow(model.probs)
marker <- "JAX00132034"
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We simulate a phenotype that is driven by the CAST (“F”) allele at a random marker:

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n.cast.alleles <- round(2*model.probs[, "F", marker])
set.seed(1)
pheno <- data.frame(simpheno1=rnorm(n, mean=n.cast.alleles))
rownames(pheno) <- animals
write.csv(pheno, file="pheno.csv", quote=F)
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We write a file of covariates (just sex in this example):

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covar <- data.frame(sex=substring(animals, 1, 1), stringsAsFactors=FALSE)
rownames(covar) <- animals
write.csv(covar, file="covar.csv", quote=F)
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