plot_internal_loop: plot_internal_loop

In RNAstructureModuleMiner: RNA Secondary Structure Comparison and Module Mining

Description

Given a RNA secondary structure,it compute internal loops in the RNA secondary structure and plots the RNA secondary structure

Usage

plot_internal_loop(ctFile)

Arguments

ctFile

A RNA secondary structure file without the first line of free energy information

Value

Return a list containing base positions in internal loops

Examples

###
col1 <- c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20)
col2 <- c("G","A","A","G","A","T","C","A","T","G","C","A","G","T","C","A","T","C","A","G")
col3 <- c(0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19)
col4 <- c(2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,0)
col5 <- c(18,17,0,15,14,13,0,0,0,0,0,0,6,5,4,0,2,1,0,0)
col6 <- c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20)
data <- matrix(c(col1,col2,col3,col4,col5,col6),byrow=FALSE,ncol =6)
data <- matrix(c(col1,col2,col3,col4,col5,col6),byrow=FALSE,ncol =6)
plot_internal_loop(data)

RNAstructureModuleMiner documentation built on May 1, 2019, 9:56 p.m.