plotReads: Plotting ranges from GRanges

In sidiropoulos/RNAprobR-old: An R package for analysis of massive parallel sequencing based RNA structure probing data

Description

Function plots cDNA inserts from GRanges created by readsamples() function. Similar to Figure 4A in HRF-Seq paper (see References).

Usage

plotReads(euc_GR, RNAid, cutoff = 1, order_by = 1, ylab, xlab, main, ylim,
  xlim, ...)

Arguments

euc_GR	GRanges generated by readsamples() function
RNAid	Transcript identifier, for which transcript plot should be generated.
cutoff	specifies cutoff length, only inserts of this length or longer will be used for processing (default: 1)
order_by	how displayed reads in plotReads function should be sorted. 1 - for sorting by termination location, 2 for sorting by reverse transcription start site
ylab	a title for the y axis: see title.
xlab	a title for the x axis: see title.
main	an overall title for the plot: see title.
xlim,ylim	numeric vectors of length 2, giving the x and y coordinates ranges.
...	Arguments to be passed to methods, such as graphical parameters (see par).

Value

Plotting function.

Author(s)

Lukasz Jan Kielpinski

References

Kielpinski, L.J., and Vinther, J. (2014). Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility. Nucleic Acids Res.

See Also

plot, plot.default, readsamples

Examples

dummy_euc_GR <- GRanges(seqnames="DummyRNA",
                        IRanges(start=round(runif(100)*100),
                        width=round(runif(100)*100+1)), strand="+",
                        EUC=round(runif(100)*100))
plotReads(dummy_euc_GR, RNAid="DummyRNA")

sidiropoulos/RNAprobR-old documentation built on May 29, 2019, 9:58 p.m.