eqtlFinder

Description

We can calculate how many eQTLs have PPA above the cutoff with the eqtlFinder function.

Usage

eqtlFinder(prob, threshold)

Arguments

Value

The output of the eqtlFinder is a data frame where the first column contains the names of each gene, the second column contains the names of corresponding markers and the third column contains the PPA value for each significant eQTL.

Examples

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

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> 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/eqtlFinder.Rd_%03d_medium.png", width=480, height=480)
> ### Name: eqtlFinder
> ### Title: eqtlFinder
> ### Aliases: eqtlFinder
> 
> ### ** Examples
> 
> data(PPA.liver)
> cutoff.liver <- calculateThreshold(PPA.liver, 0.2)
> eqtl.liver <- eqtlFinder(PPA.liver, cutoff.liver)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>