RRNA (version 1.2)

loadCt: 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)

Value

Returns at data frame containing the CT file data

Arguments

file

The name of the CT file being loaded

Author

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 ###

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

ctfile=loadCt(f)

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

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