loadCt: Loads a CT file into an R data frame

In jpbida/RRNA: Secondary Structure Plotting for RNA

Loads a CT file into an R data frame

Description

A variety of RNA secondary structure prediction programs produce CT files. You can load these CT files into R using the loadCT function.

Usage

loadCt(file)

Arguments

file	The name of the CT file being loaded

Value

Returns at data frame containing the CT file data

Author(s)

JP Bida

See Also

RNAPlot aptPlotCT

Examples

### Create a CT file with PseudoKnots ###
pk=makeCt("((((...(((((((.........)))))))...((((.........))))...))))",
          "AAAAAAAACCCCCCCCAAAGGGGGGGAUUACCCCUCCUUUAAAAGGGUUUUCCCCCCC"
         )
pk$bound[pk$pos==20]=42
pk$bound[pk$pos==19]=43
pk$bound[pk$pos==43]=19
pk$bound[pk$pos==42]=20

### Create a CT file for testing ###

ctfile = tempfile(fileext = ".ct")

write.table(pk[,c(1,4,2,3,6,5)],file=ctfile,
            row.names=FALSE,col.names=TRUE)

ctfile=loadCt(ctfile)

### Before using ct2coord you need to remove the pseudo knots ###

l=pseudoKnot(ctfile)
dat=l[[2]]
cd=ct2coord(dat)
RNAPlot(cd)

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