print-methods {podkat} | R Documentation

## Print Association Test Results

### Description

Display method for S4 class `AssocTestResultRanges`

### Usage

    ## S4 method for signature 'AssocTestResultRanges'
    print(x, cutoff=0.05,
            sortBy=c("p.value", "p.value.adj", "p.value.resampled",
                     "p.value.resampled.adj", "genome", "none"),
            max.show=10)

### Arguments

`x` | an object of class `AssocTestResultRanges`
`cutoff` | a numerical vector with one or more p-value thresholds; if present (otherwise `NA` or an empty vector must be passed), `print` displays the number of tested regions with a p-value below each threshold. If the `AssocTestResultRanges` object also contains adjusted p-values, the numbers of tested regions with p-values below each of the thresholds are printed too. If `max.show` is greater than 0, the `max.show` most significant regions up to an (adjusted) p-value (depending on the `sortBy` argument) up to the largest threshold are shown.
`sortBy` | a character string that determines (1) how regions are sorted and (2) according to which p-value the `cutoff` threshold is applied when printing regions; if `sortBy` is “p.value” (default), regions are sorted according to raw p-values and only the `max.show` most significant regions are printed - as long as the raw p-value is not larger than the largest value in the `cutoff` argument. For “p.value.adj”, regions are sorted and filtered according to adjusted p-values, analogously for choices “p.value.resampled” and “p.value.resampled.adj”. In case that `sortBy` is “genome”, the p-values are ignored and the first `max.show` regions in the genome are displayed. In case that `sortBy` is “none”, the p-values are also ignored and the first `max.show` regions are displayed in the order as they appear in the `AssocTestResultRanges` object.
`max.show` | maximum number of regions to display; if 0, no regions are displayed at all.

### Details

`print` displays the most important information stored in an `AssocTestResultRanges` object `x`. That includes the type of null model, the numbers of samples and tested regions, the kernel that was used for testing, etc. Depending on the `cutoff` argument, a certain number of significant tests is printed. If `max.show` is larger than 0, then some regions are shown along with association test results. Which regions are selected and how they are sorted, depends on the arguments `sortBy` and `cutoff` (see above).

### Value

`print` returns its argument `x` invisibly.

### Author(s)

Ulrich Bodenhofer bodenhofer@bioinf.jku.at

### References

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

### See Also

`GenotypeMatrix`, `NullModel`, `AssocTestResult`, `AssocTestResultRanges`

### Examples

    ## load genome description
    data(hgA)

    ## partition genome into overlapping windows
    windows <- partitionRegions(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 multiple regions
    res <- assocTest(Z, nm.lin, windows)

    ## perform multiple testing correction
    res.adj <- p.adjust(res)

    ## print 'AssocTestResultRanges' object
    print(res)
    print(res, max.show=0)
    print(res.adj, cutoff=c(0.005, 0.01, 0.05))
    print(res.adj, cutoff=0.05, sortBy="p.value.adj")
    print(res.adj, cutoff=NA, sortBy="none", max.show=40)

[Package podkat version 1.14.0 Index]