plotRNA: Plot normalized values over transcript positions

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

Description

Function plotting normalized values over transcript positions.

Usage

plotRNA(norm_GR, RNAid, norm_method, stat_method, stat_cutoff, main, type, ylab,
  xlab, ...)

Arguments

norm_GR	norm_GR GRanges with data to be exported, required
RNAid	Transcript identifier, for which transcript plot should be generated.
norm_method	Which normalization method should be to be used for plotting (column name).
stat_method	Name of a column to be used for adding significance asterisks. If stat_method not provided, function tries to match with "norm_method", if no guess - empty vector.
stat_cutoff	below what value of statistics (from stat_method, p-value or standard deviation) report significance. If not provided - minimal value from stat_method used. To suppress reporting significant sites provide negative value
main	an overall title for the plot: see title.
type	what type of plot should be drawn. See plot for possible types.
ylab	a title for the y axis: see title.
xlab	a title for the x axis: see title.
...	Arguments to be passed to methods, such as graphical parameters (see par).

Value

Plotting function.

Author(s)

Lukasz Jan Kielpinski

See Also

plot, plot.default, dtcr, slograt, swinsor, compdata

Examples

dummy_euc_GR_treated <- GRanges(seqnames="DummyRNA",
                                IRanges(start=round(runif(100)*100),
                                width=round(runif(100)*100+1)), strand="+",
                                EUC=round(runif(100)*100))
dummy_comp_GR_treated <- comp(dummy_euc_GR_treated)
dummy_swinsor <- swinsor(dummy_comp_GR_treated)
plotRNA(dummy_swinsor, RNAid="DummyRNA")

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