plotVariantsForCNV: plotVariantsForCNV

In CNVfilteR: Identifies false positives of CNV calling tools by using SNV calls

Description

Plots a CNV with all the variants in it

Usage

plotVariantsForCNV(
  cnvfilter.results,
  cnv.id,
  points.cex = 1,
  points.pch = 19,
  legend.x.pos = 0.08,
  legend.y.pos = 0.25,
  legend.cex = 0.8,
  karyotype.cex = 1,
  cnv.label.cex = 1,
  x.axis.bases.cex = 0.7,
  x.axis.bases.digits = 5,
  y.axis.title.cex = 0.8,
  y.axis.label.cex = 0.8,
  cnv.zoom.margin = TRUE
)

Arguments

cnvfilter.results	S3 object returned by filterCNVs function
cnv.id	CNV id for which to plot variants
points.cex	Points cex (size). (Defaults to 1)
points.pch	Points pch (symbol). (Defaults to 19)
legend.x.pos	Legend x position. (Defaults to 0.08)
legend.y.pos	Legend y position. (Defaults to 0.25)
legend.cex	Legend cex. (Defaults to 0.8)
karyotype.cex	karyotype cex: affects top title and chromosome text (at bottom). (Defaults to 1)
cnv.label.cex	"CNV" text cex. (Defaults to 1)
x.axis.bases.cex	X-axis bases position cex. (Defaults to 0.7)
x.axis.bases.digits	X-axis bases position number of digits. (Defaults to 5)
y.axis.title.cex	Y-axis title cex. (Defaults to 0.8)
y.axis.label.cex	Y-axis labels cex. (Defaults to 0.8)
cnv.zoom.margin	If TRUE, the zoom leaves an small margin at both sides of the CNV. False otherwise. (Defaults to TRUE)

Value

invisibly returns a karyoplot object

Examples

# Load CNVs data
cnvs.file <- system.file("extdata", "DECoN.CNVcalls.csv", package = "CNVfilteR", mustWork = TRUE)
cnvs.gr <- loadCNVcalls(cnvs.file = cnvs.file, chr.column = "Chromosome", start.column = "Start", end.column = "End", cnv.column = "CNV.type", sample.column = "Sample")

# Load VCFs data
vcf.files <- c(system.file("extdata", "variants.sample1.vcf.gz", package = "CNVfilteR", mustWork = TRUE),
               system.file("extdata", "variants.sample2.vcf.gz", package = "CNVfilteR", mustWork = TRUE))
vcfs <- loadVCFs(vcf.files, cnvs.gr = cnvs.gr)

# Filter CNVs
results <- filterCNVs(cnvs.gr, vcfs)

# Check CNVs that can be filtered out
as.data.frame(results$cnvs[results$cnvs$filter == TRUE])

# Plot one of them
plotVariantsForCNV(results, "3")

CNVfilteR documentation built on April 17, 2021, 6:06 p.m.