Description Usage Arguments Details Value Author(s) Examples
View source: R/plotobservedsnps.R
Given an average depth of coverage and per base sequencing error rate, estimate the read frequency of most common polymorphic sites.
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data |
Full sequence data generated from the |
timepoint |
Which sampling time should be used. |
coverage |
Coverage depth. |
error |
Sequencing erorr rate per base. |
iterations |
Number of iterations to generate confidence bounds. |
maxsnp |
Number of polymorphic sites to show. |
legend |
Should a legend be plotted? |
ylim |
Bounds of y axis. |
... |
Additional arguments to be passed to |
Plots the expected number of reads containing the most frequent polymorphisms, with a 95% confidence interval, derived from repeated random draws. Additionally shows the frequency of false positive observations arising through sequencing error.
Returns an iterations
x maxsnp
matrix. Each column represents a polymorphic site, and each row one iteration. Each entry provides the number of reads containing the polymorphism in a given iteration. Columns are ordered by frequency.
T. D. Read (tread@emory.edu)
1 2 3 4 5 6 7 8 | data(deepseq)
# At the 25th time point
plotobservedsnps(data=deepseq, timepoint=25, xaxt="n", xlab="Ranked polymorphic sites",
ylab="Reads", yaxs="i", las=1)
# At the 50th time point
plotobservedsnps(data=deepseq, timepoint=50, xaxt="n", xlab="Ranked polymorphic sites",
ylab="Reads", yaxs="i", las=1)
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