Also plotted are confidence intervals for the expected count, and the actual observed number of peaks per gene.
plot_expected_peaks(peaks, locusdef = "nearest_tss", genome = "hg19", use_mappability = F, read_length = 36, mappa_file = NULL
)
supported_locusdefs
for a list of supported definitions.
supported_genomes
function.
locusdef
.) The y-axis is count of peaks. Each blue dot represents the observed count of peaks assigned to a gene. The black line represents the expected number of peaks given locus length.
Also drawn are the 5 and 95% percentiles of a Poisson distribution for the expected number of peaks, and the 5 and 95% percentiles adjusted for the number of genes (Bonferroni adjustment - e.g. 0.05 / # of genes.)
chipenrich
library(chipenrich.data)
library(chipenrich)
# Expected peak count plot for the E2F4 dataset.
data(peaks_E2F4)
plot_expected_peaks(peaks_E2F4,genome='hg19')
# Create the plot for a different locus definition
# to compare the effect.
plot_expected_peaks(peaks_E2F4,locusdef='nearest_gene',genome='hg19');
# Create the plot, but write the result to a PDF
# instead of displaying it interactively.
pdf("expected_peak_plot.pdf");
p = plot_expected_peaks(peaks_E2F4,genome='hg19');
dev.off();
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