compare: compare

In RNAstructureModuleMiner: RNA Secondary Structure Comparison and Module Mining

Description

return similarity score of two RNA secondary structure

Usage

compare(ctFile1,ctFile2)

Arguments

ctFile1	A RNA secondary structure file without the first line of free energy information
ctFile2	A RNA secondary structure file without the first line of free energy information

Value

Returns a numerical value which represent the similarity of the two RNA secondary structures.The larger the value, the more similar the two RNA structures are.The maximum value is 10, representing the two RNA secondary structures exactly the same,and 0 is the minmum value.

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)

col1_2 <- c(1,2,3,4,5,6,7,8,9,10,11,12,13)
col2_2 <- c("G","A","C","U","G","G","G","G","C","G","G","U","C")
col3_2 <- c(0,1,2,3,4,5,6,7,8,9,10,11,12)
col4_2 <- c(2,3,4,5,6,7,8,9,10,11,12,13,0)
col5_2 <- c(13,12,11,10,9,0,0,0,5,4,3,2,1)
col6_2 <- c(1,2,3,4,5,6,7,8,9,10,11,12,13)
data1 <- matrix(c(col1,col2,col3,col4,col5,col6),byrow=FALSE,ncol = 6)
data2 <- matrix(c(col1_2,col2_2,col3_2,col4_2,col5_2,col6_2),byrow=FALSE,ncol = 6)
compare(data1,data2)

Example output

Loading required package: RRNA

Attaching package: 'RNAstructureModuleMiner'

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

    stem

[1] 6.119048

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