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Last data update: 2014.03.03

R: Plot normalized values over transcript positions

plotRNA

R Documentation

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.

Author(s)

Lukasz Jan Kielpinski

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")

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(RNAprobR)
Loading required package: GenomicFeatures
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: plyr

Attaching package: 'plyr'

The following object is masked from 'package:IRanges':

    desc

The following object is masked from 'package:S4Vectors':

    rename

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RNAprobR/plotRNA.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotRNA
> ### Title: Plot normalized values over transcript positions
> ### Aliases: plotRNA
> 
> ### ** 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)
Fasta file not specified.
0 % of EUCs removed due to cutoff
> dummy_swinsor <- swinsor(dummy_comp_GR_treated)
> plotRNA(dummy_swinsor, RNAid="DummyRNA")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>