plotEQTL: Plot EQTL region

In waldronlab/CNVRanger: Summarization and expression/phenotype association of CNV ranges

Plot EQTL region

Description

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

Usage

plotEQTL(cnvr, genes, genome, cn = "CN1", cex = 0.8)

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.
cex	A numerical value giving the amount by which gene names should be magnified. Default is 0.8. Use smaller values to decrease font size.

Value

None. Plots to a graphics device.

Author(s)

Ludwig Geistlinger

See Also

Gviz::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")

waldronlab/CNVRanger documentation built on Nov. 1, 2024, 7:11 a.m.