AssocTestResult-class | R Documentation |

`AssocTestResult`

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

Objects of this class are created by calling `assocTest`

for a single genomic region.

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

- 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.

Ulrich Bodenhofer bodenhofer@bioinf.jku.at

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

`assocTest`

## 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)

UBod/podkat documentation built on Nov. 17, 2022, 6:45 p.m.

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.