plotEQTL {CNVRanger} | R Documentation

## Plot EQTL region

### Description

Illustrates differential expression of genes in the neighborhood of a CNV.

### Usage

    plotEQTL(cnvr, genes, genome, cn = "CN1")

### Arguments

`cnvr` | A `GRanges` of length 1, containing the genomic coordinates of the CNV region of interest.
`genes` | `GRanges` containing genes in the neighborhood of the CNV region of interest.
`genome` | Character. A valid UCSC genome assembly ID such as 'hg19' or 'bosTau6'.
`cn` | Character. Copy number state of interest.

### Value

None. Plots to a graphics device.

### Author(s)

Ludwig Geistlinger

### See Also

`plotTracks`

### Examples

    # CNV region of interest
    cnvr <- GRanges("chr1:7908902-8336254")

    # Two genes in the neighborhood
    genes <- c("chr1:8021714-8045342:+", "chr1:8412464-8877699:-")
    names(genes) <- c("PARK7", "RERE")
    genes <- GRanges(genes)

    # Annotate differential expression for 1-copy loss
    genes$logFC.CN1 <- c(-0.635, -0.728)
    genes$AdjPValue <- c(8.29e-09, 1.76e-08)

    # plot
    plotEQTL(cnvr, genes, genome="hg19", cn="CN1")

[Package CNVRanger version 1.0.3 Index]