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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

getMafCutoff(x, ...)

getMacCutoff(x, ...)

getXvarCutoff(x, ...)

getImissCutoff(x, ...)

getKeepVariants(x, ...)

getKeepIndel(x, ...)

# S4 method for class 'QtlDataset'
getMafCutoff(x, ...)

# S4 method for class 'QtlDataset'
getMacCutoff(x, ...)

# S4 method for class 'QtlDataset'
getXvarCutoff(x, ...)

# S4 method for class 'QtlDataset'
getImissCutoff(x, ...)

# S4 method for class 'QtlDataset'
getKeepVariants(x, ...)

# S4 method for class 'QtlDataset'
getKeepIndel(x, ...)

Arguments

x

A QtlDataset.

...

Additional arguments passed on to methods.

Value

getMafCutoff(), getMacCutoff(), getXvarCutoff() and getImissCutoff() single numerics; getKeepVariants() a character vector (empty when no restriction was requested); getKeepIndel() a single logical. The sample set is not among them: it lives in colData(x) and sampleMap(x).

Examples

data(qtlDatasetExample)
getMafCutoff(qtlDatasetExample)
#> [1] 0
getKeepIndel(qtlDatasetExample)
#> [1] TRUE