S4 class for storing the result of an association test for a single genomic region
Objects of this class are created by calling
for a single genomic region.
The following slots are defined for
type of null model on which the association test was based
character vector with sample names (if available, otherwise empty)
kernel that was used for the association test
dimensions of genotype matrix that was tested
weight vector that was used; empty if no weighting was performed
tolerance radius parameter that was used for position-dependent kernels
method(s) used to compute p-values; a single character string if no resampling was done, otherwise a list with two components specifying the p-value computation method for the test's p-value and the resampled p-values separately.
a logical vector indicating whether the
small sample correction was carried out (first component
TRUE) and/or higher moment correction was carried
out (second component
the test's p-value
test statistics for sampled null model residuals
p-values for sampled null model residuals
estimated p-value computed as the relative frequency of p-values of sampled residuals that are at least as significant as the test's p-value
the matched call with which the object was created
displays the test statistic and the p-value along with the type of
the null model, the number of samples, the number of SNVs, and the
kernel that was used to carry out the test.
Ulrich Bodenhofer [email protected]
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## 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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