iBMQ (version 1.12.0)

hotspotFinder: hotspotFinder

Description

One main advantage of our method is its increased sensitivity for finding trans-eQTL hotspots (corresponding to situations where a single SNP is linked to the expression of several genes across the genome).

Usage

hotspotFinder(peak, numgene)

Arguments

peak

A data frame (3 columns) corresponding to the output of the eqtlFinder function or the data frame (9 columns) corresponding to the output of the eqtlClassifier function.

numgene

The minimum of gene to detect.

Value

The output of this function is a list, where each element is a marker. For each marker there is a data frame with all the eQTLs linked to this marker.

Examples

data(PPA.liver)
cutoff.liver <- calculateThreshold(PPA.liver, 0.2)
eqtl.liver <- eqtlFinder(PPA.liver, cutoff.liver)
hotspot.liver <- hotspotFinder(eqtl.liver,20)