Secondary Structure Plotting for RNA

Documentation for package ‘RRNA’ version 1.0

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