lodPeaks: LOD score peaks

In paramlink2: Parametric Linkage Analysis

LOD score peaks

Description

Identify and summarise LOD score peaks.

Usage

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

# 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 Feb. 16, 2023, 6:05 p.m.