plot.bed {BayesPeak} | R Documentation |
Plot the distribution of reads in a .bed file.
plot.bed(x, chr, start, end, strand = "+", bin = 50L, ...)
x |
RangedData (from the IRanges package) with a value column entitled |
chr |
Character. Chromosome to plot - should be exactly the same as a space in |
start, end |
Integer. Start and end locations on chromosome. |
strand |
Character. Strand to plot - usually either "+" or "-". If the |
bin |
Integer. The width of bin to plot. |
... |
Additional arguments, passed to |
This function takes the reads in a bed file, and plots a histogram of their locations. This allows us to see the peaks present in the data.
Plots a histogram on the active graphical device.
Jonathan Cairns
Spyrou C, Stark R, Lynch AG, Tavare S BayesPeak: Bayesian analysis of ChIP-seq data, BMC Bioinformatics 2009, 10:299 doi:10.1186/1471-2105-10-299
dir <- system.file("extdata", package="BayesPeak") treatment <- file.path(dir, "H3K4me3reduced.bed") bed <- read.bed(treatment) ##look at region chr16:91000000-94000000 plot.bed(bed, "chr16", 9.1E7, 9.4E7)