AssocTestResult-class: Class 'AssocTestResult'

In podkat: Position-Dependent Kernel Association Test

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.

Slots

The following slots are defined for AssocTestResult objects:

type:

type of null model on which the association test was based

samples:

character vector with sample names (if available, otherwise empty)

kernel:

kernel that was used for the association test

dim:

dimensions of genotype matrix that was tested

weights:

weight vector that was used; empty if no weighting was performed

width:

tolerance radius parameter that was used for position-dependent kernels

method:

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.

correction:

a logical vector indicating whether the small sample correction was carried out (first component exact is TRUE) and/or higher moment correction was carried out (second component resampling is TRUE).

Q:

test statistic

p.value:

the test's p-value

Q.resampling:

test statistics for sampled null model residuals

p.value.resampling:

p-values for sampled null model residuals

p.value.resampled:

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

call:

the matched call with which the object was created

Methods

show

signature(object="AssocTestResult"): 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.

Author(s)

Ulrich Bodenhofer [e-mail]

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)

podkat documentation built on Nov. 8, 2020, 6:55 p.m.