plotEQTL: Plot EQTL region
In CNVRanger: Summarization and expression/phenotype association of CNV ranges

Description Usage Arguments Value Author(s) See Also Examples

View source: R/expr_assoc.R

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

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

`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.

None. Plots to a graphics device.

Ludwig Geistlinger

Gviz::plotTracks

# 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")