paramlink2 (version 1.0.6)

lodPeaks: LOD score peaks

Description

Identify and summarise LOD score peaks.

Usage

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

Value

A list of data frames.

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.

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)