pseudoKnot {RRNA}

removes pseudoknots from a ct file

Description

internal function used to remove pseudoKnots before calling ct2coord

Usage

pseudoKnot(ctDat)

Arguments

ctDat

R data frame representing a CT file for RNA secondary structure

Value

Returns a list with the first item being a list of pseudoKnots and the second item being a CT file data frame with all pseudoKnots removed from the structure

Author(s)

JP Bida

See Also

RNAPlot, aptPlotCT, ct2coord,

Examples

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

l=pseudoKnot(pk)

## Positions of removed pseudo knots ##
removed=l[[1]]

### clean ct file that can be used by ct2coord ###
ct=l[[2]]