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RRNA (version 1.0)

Secondary Structure Plotting for RNA

Description

Functions for creating and manipulating RNA secondary structure plots.

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Version

Install

install.packages('RRNA')

Monthly Downloads

271

Version

1.0

License

GPL-3

Maintainer

JP Bida

Last Published

July 29th, 2015

Functions in RRNA (1.0)

genCords

Internal function that generates coordinates for a given loop starting and stopping at p1 and p2 respectfully

alignCoord

Alignment of secondary structure folds to 2 nucleotides.

aptPlotCT

RNA secondary structure plotting from CT files

RNAPlot

Generic RNA Secondary Structure Plotting Function

makeCt

make a CT file from a structure and sequence

translate

internal function for translating points

bplfile

Creates a bpl file from a coordinate file

ct2knet

creates a knet file from a CT file

RRNA-package

RNA secondary structure ploting

ct2coord

Generate coordinate file

forward

Internal function for moving through secondary structures

backward

Internal function for moving through secondary structures

circleCoord

Internal function for finding the coordinates of NT's in a circle

stemCords

internal function that generates coordinates for a stem

loadCt

Loads a CT file into an R data frame

loadCoords

Loads a coordinate file into a data frame

rotateV

internal function to rotate a vector of points

pseudoKnot

removes pseudoknots from a ct file

transformFold

Internal function to translate and rotate a secondary structure plot

rotateS

Internal function to rotate a single point

loopLength

internal function that determines the length of a loop