checkProbes: Check Probe Specificity for Some Regions

In Repitools: Epigenomic tools

Description

Given a set of gene coordinates, and probe mappings to the genome, a plot is created across every gene region of how many probes mapped to each position.

Usage

  ## S4 method for signature 'data.frame,data.frame'
checkProbes(regs, probes, up = NULL, down = NULL, ...)
  ## S4 method for signature 'GRanges,GRanges'
checkProbes(regs, probes, up = NULL, down = NULL, ...)

Arguments

regs	A data.frame with (at least) columns chr, start, end, strand, and name, or a GRanges object with an elementMetadata column name. The starts and ends of regions describe are the windows plotted in.
probes	A data.frame describing where the probes mapped to, with (at least) columns name (identifier of a probe), chr, start, and end, or a GRanges object with an elementMetadata column name.
up	How many bases upstream to plot.
down	How many bases downstream to plot.
...	Line parameters passed onto matplot.

Details

If up and down are NULL, then the gene is plotted as it is described by its start and end coordinates.

This function produces a number of plots. Sending output to a PDF device is recommended.

Value

A set of plots is created, one for each of the genes. The lines in the plot show where a probe hits (the x - axis) and how many places in total the probe hits in the genome (y - axis).

Author(s)

Dario Strbenac

Examples

	p.table <- data.frame(name = c("probeA", "probeB", "probeC", "probeC", "probeC"),
			    strand = c('+', '-', '+', '-', '-'),
                               chr = c("chr1", "chr2", "chr1", "chr2", "chr2"),
                             start = c(20, 276, 101, 101, 151),
                               end = c(44, 300, 125, 125, 175))
	r.table <- data.frame(name = c("gene1", "gene2", "gene3"),
                               chr = c("chr1", "chr2", "chr2"),
                            strand = c('+', '-', '+'),
                             start = c(20, 500, 75),
                               end = c(200, 800, 400))
	pdf("tmp.pdf", height = 6, width = 14)
	checkProbes(r.table, p.table, lwd = 4, col = "blue")
	dev.off()

Repitools documentation built on Nov. 8, 2020, 7:52 p.m.