R: Secondary Structure Plotting for RNA

# Secondary Structure Plotting for RNA

## Documentation for package ‘RRNA’ version 1.2

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

RRNA-package | RNA secondary structure ploting
alignCoord | Alignment of secondary structure folds to 2 nucleotides.
aptPlotCT | RNA secondary structure plotting from CT files
backward | Internal function for moving through secondary structures
bplfile | Creates a bpl file from a coordinate file
circleCoord | Internal function for finding the coordinates of NT's in a circle
ct2coord | Generate coordinate file
ct2knet | creates a knet file from a CT file
forward | Internal function for moving through secondary structures
genCords | Internal function that generates coordinates for a given loop starting and stopping at p1 and p2 respectfully
loadCoords | Loads a coordinate file into a data frame
loadCt | Loads a CT file into an R data frame
loopLength | internal function that determines the length of a loop
makeCt | make a CT file from a structure and sequence
pseudoKnot | removes pseudoknots from a ct file
RNAPlot | Generic RNA Secondary Structure Plotting Function
rotateS | Internal function to rotate a single point
rotateV | internal function to rotate a vector of points
RRNA | RNA secondary structure ploting
stemCords | internal function that generates coordinates for a stem
transformFold | Internal function to translate and rotate a secondary structure plot
translate | internal function for translating points