plotRNA: Plot normalized values over transcript positions

Description Usage Arguments Value Author(s) See Also Examples

View source: R/finishing.R

Description

Function plotting normalized values over transcript positions.

Usage

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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

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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")

RNAprobR documentation built on Nov. 22, 2017, 2 a.m.