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

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(iBMQ)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/iBMQ/hotspotFinder.Rd_%03d_medium.png", width=480, height=480)
> ### Name: hotspotFinder
> ### Title: hotspotFinder
> ### Aliases: hotspotFinder
> 
> ### ** Examples
> 
> data(PPA.liver)
> cutoff.liver <- calculateThreshold(PPA.liver, 0.2)
> eqtl.liver <- eqtlFinder(PPA.liver, cutoff.liver)
> hotspot.liver <- hotspotFinder(eqtl.liver,20)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>