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QtlDataset Filter Settings

Source: R/AllGenerics.R, R/QtlDataset.R
qtlDatasetFilters.Rd

The variant- and sample-filter settings a QtlDataset was built with. They are recorded on the object rather than reapplied per call, so reading them back is how a caller finds out what a dataset already excludes.

Usage

mafCutoff(x, ...)

macCutoff(x, ...)

xvarCutoff(x, ...)

imissCutoff(x, ...)

keepVariants(x, ...)

keepIndel(x, ...)

# S4 method for class 'QtlDataset'
mafCutoff(x)

# S4 method for class 'QtlDataset'
macCutoff(x)

# S4 method for class 'QtlDataset'
xvarCutoff(x)

# S4 method for class 'QtlDataset'
imissCutoff(x)

# S4 method for class 'QtlDataset'
keepVariants(x)

# S4 method for class 'QtlDataset'
keepIndel(x)

Arguments

x

A QtlDataset.

...

Additional arguments passed on to methods.

Value

mafCutoff(), macCutoff(), xvarCutoff() and imissCutoff() single numerics; keepVariants() a character vector (empty when no restriction was requested); keepIndel() a single logical. The sample set is not among them: it lives in colData(x) and sampleMap(x).

Examples

data(qtlDatasetExample)
mafCutoff(qtlDatasetExample)
#> [1] 0
keepIndel(qtlDatasetExample)
#> [1] TRUE