An R package for RNA visualization and analysis

Description

An R package for RNA visualization and analysis

Examples

    # Read input data
    predicted <- readHelix(system.file("extdata", "helix.txt", package = "R4RNA"))
    known <- readVienna(system.file("extdata", "vienna.txt", package = "R4RNA"))
    sequence <- as.character(readBStringSet(system.file("extdata", "fasta.txt", package = "R4RNA")))

    plotHelix(predicted)
    pval.coloured <- colourByValue(predicted, log = TRUE, get = TRUE)
    plotDoubleHelix(pval.coloured, known, scale = FALSE)
    plotOverlapHelix(pval.coloured, known)

    cov.coloured <- colourByCovariation(known, sequence, get = TRUE)
    plotCovariance(sequence, cov.coloured)
    
    plotDoubleCovariance(cov.coloured, pval.coloured, sequence,
        conflict.filter = "grey")
    plotOverlapCovariance(pval.coloured, known, sequence, grid = TRUE,
        conflict.filter = "grey", legend = FALSE, any = TRUE)

    # List of all functions
    ls("package:R4RNA")
    # use example() and help() for more details on each function

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.
You are welcome to redistribute it under certain conditions.
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(R4RNA)
Loading required package: Biostrings
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: XVector
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/R4RNA/R4RNA-package.Rd_%03d_medium.png", width=480, height=480)
> ### Name: R4RNA-package
> ### Title: An R package for RNA visualization and analysis
> ### Aliases: R4RNA R4RNA-package
> ### Keywords: package
> 
> ### ** Examples
> 
>     # Read input data
>     predicted <- readHelix(system.file("extdata", "helix.txt", package = "R4RNA"))
>     known <- readVienna(system.file("extdata", "vienna.txt", package = "R4RNA"))
>     sequence <- as.character(readBStringSet(system.file("extdata", "fasta.txt", package = "R4RNA")))
> 
>     plotHelix(predicted)
>     pval.coloured <- colourByValue(predicted, log = TRUE, get = TRUE)
>     plotDoubleHelix(pval.coloured, known, scale = FALSE)
>     plotOverlapHelix(pval.coloured, known)
> 
>     cov.coloured <- colourByCovariation(known, sequence, get = TRUE)
>     plotCovariance(sequence, cov.coloured)
>     
>     plotDoubleCovariance(cov.coloured, pval.coloured, sequence,
+         conflict.filter = "grey")
>     plotOverlapCovariance(pval.coloured, known, sequence, grid = TRUE,
+         conflict.filter = "grey", legend = FALSE, any = TRUE)
> 
>     # List of all functions
>     ls("package:R4RNA")
 [1] "alignmentCanonical"        "alignmentConservation"    
 [3] "alignmentCovariation"      "alignmentPercentGaps"     
 [5] "as.helix"                  "baseConservation"         
 [7] "basepairCanonical"         "basepairConservation"     
 [9] "basepairCovariation"       "basepairFrequency"        
[11] "blankPlot"                 "collapseHelix"            
[13] "colourByBasepairFrequency" "colourByCanonical"        
[15] "colourByConservation"      "colourByCount"            
[17] "colourByCovariation"       "colourByUnknottedGroups"  
[19] "colourByValue"             "defaultPalette"           
[21] "expandHelix"               "helixCanonical"           
[23] "helixConservation"         "helixCovariation"         
[25] "helixToBpseq"              "helixToConnect"           
[27] "helixToVienna"             "is.helix"                 
[29] "isConflictingHelix"        "isDuplicatingHelix"       
[31] "isOverlappingHelix"        "logceiling"               
[33] "logfloor"                  "logseq"                   
[35] "maxHeight"                 "plotArc"                  
[37] "plotArcs"                  "plotCovariance"           
[39] "plotDoubleCovariance"      "plotDoubleHelix"          
[41] "plotHelix"                 "plotOverlapCovariance"    
[43] "plotOverlapHelix"          "readBpseq"                
[45] "readConnect"               "readHelix"                
[47] "readVienna"                "structureMismatchScore"   
[49] "unknottedGroups"           "viennaToHelix"            
[51] "writeHelix"               
>     # use example() and help() for more details on each function
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>