podkat (version 1.4.2)

print-methods: Print Association Test Results

Description

Display method for S4 class AssocTestResultRanges

Usage

## S3 method for class '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.

Value

• print returns its argument x invisibly.

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).

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)