plotReads: Plotting ranges from GRanges

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/finishing.R

Description

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

Usage

1
2
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

1
2
3
4
5
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")

RNAprobR documentation built on May 31, 2017, 10:52 a.m.