lodPeaks: LOD score peaks

Description Usage Arguments Details Value See Also Examples

View source: R/peak_utils.R

Description

Identify and summarise LOD score peaks.

Usage

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lodPeaks(x, threshold, width = 1)

peakSummary(x, threshold, width = 1, physmap = NULL)

Arguments

x

A linkres object, or data frame with columns CHROM, MB, LOD.

threshold

A single number

width

A positive integer

physmap

A matrix or data frame with three columns: Marker name, chromosome and physical position.

Details

A peak is defined as a run of at least width consecutive markers with LOD score above or equal to threshold. If possible, one flanking marker is included on each side of the peak.

Value

A list of data frames.

See Also

linkres, lod(), merlinLod()

Examples

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# Use built-in dataset `dominant1`
lods = lod(x = dominant1$ped,
           aff = dominant1$aff,
           model = diseaseModel("AD"))

# All peaks above LOD = 1.5
lodPeaks(lods, threshold = 1.5)
peakSummary(lods, threshold = 1.5)

paramlink2 documentation built on May 5, 2021, 1:08 a.m.