hairpin_loop: hairpin_loop

In RNAstructureModuleMiner: RNA Secondary Structure Comparison and Module Mining

Description

Given a RNA secondary structure,it compute hairpin loops in the RNA secondary structure

Usage

hairpin_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 hairpin loops,and the length of the number of hairpin loops

Examples

###
col1 <- c(1,2,3,4,5,6,7,8,9,10,11,12,13)
col2 <- c("G","A","C","U","G","G","G","G","C","G","G","U","C")
col3 <- c(0,1,2,3,4,5,6,7,8,9,10,11,12)
col4 <- c(2,3,4,5,6,7,8,9,10,11,12,13,0)
col5 <- c(13,12,11,10,9,0,0,0,5,4,3,2,1)
col6 <- c(1,2,3,4,5,6,7,8,9,10,11,12,13)
data <- matrix(c(col1,col2,col3,col4,col5,col6),byrow=FALSE,ncol = 6)
hairpin_loop(data)

Example output

Loading required package: RRNA

Attaching package: 'RNAstructureModuleMiner'

The following object is masked from 'package:graphics':

    stem

[[1]]
[1] 6 7 8

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