RNAprobR (version 1.4.0)

plotRNA: Plot normalized values over transcript positions

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.

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")