AssocTestResult-class {podkat} | R Documentation

## 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.

### 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 bodenhofer@bioinf.jku.at

### 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)

[Package podkat version 1.18.0 Index]