loadCoords: Loads a coordinate file into a data frame

In jpbida/RRNA: Secondary Structure Plotting for RNA

Loads a coordinate file into a data frame

Description

Coordinate files can be created from the viennaRNA library.

Usage

loadCoords(filename)

Arguments

filename

Name of the coordinate file being loaded

Value

Data frame containing the coordinate file

Author(s)

JP Bida

References

The RRNAFold program generates the coordinate files used by RRNA

https://github.com/jpbida/ViennaScripts

Examples

### Create a test coordinate file using ct2coord ###
ct=makeCt("((((...(((((((.........)))))))...((((.........))))...))))",
          "AAAAAAAACCCCCCCCAAAGGGGGGGAUUACCCCUCCUUUAAAAGGGUUUUCCCCCCC" 
         )
coord=ct2coord(ct)
### add an id ###
coord$id=1
### write out test file ###
crfile = tempfile(fileext=".cr")

write.table( coord[,c('id','x','y','seq','num','bound')],
             col.names=FALSE,row.names=FALSE,sep=",",file=crfile
           )

### Read in the coordinate file ##
input=loadCoords(crfile)
  
### Plot the file using RNAPlot ##
RNAPlot(input)

jpbida/RRNA documentation built on April 28, 2024, 1:27 p.m.