checkProbes {Repitools} | R Documentation |
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.
## 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, ...)
regs |
A |
probes |
A |
up |
How many bases upstream to plot. |
down |
How many bases downstream to plot. |
... |
Line parameters passed onto |
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.
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).
Dario Strbenac
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()