podkat (version 1.4.2)

AssocTestResult-class: Class AssocTestResult

Description

S4 class for storing the result of an association test for a single genomic region

Objects

Objects of this class are created by calling assocTest for a single genomic region.

References

http://www.bioinf.jku.at/software/podkat

See Also

assocTest

Examples

## load genome description
data(hgA)

## load genotype data from VCF file
vcfFile <- system.file("examples/example1.vcf.gz", package="podkat")
Z <- readGenotypeMatrix(vcfFile)

## read phenotype data from CSV file (continuous trait + covariates)
phenoFile <- system.file("examples/example1lin.csv", package="podkat")
pheno <-read.table(phenoFile, header=TRUE, sep=",")

## train null model with all covariates in data frame 'pheno'
nm.lin <- nullModel(y ~ ., pheno)

## perform association test for entire genotype matrix
res <- assocTest(Z, nm.lin)
show(res)

## perform association test for subset of genotype matrix
res <- assocTest(Z[, 50:100], nm.lin)
show(res)

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