Description Usage Arguments Value Examples
Given a RNA secondary structure,it compute stems in the RNA secondary structure and plots the RNA secondary structure
1 | plot_stem(ctFile)
|
ctFile |
A RNA secondary structure file without the first line of free energy information |
Return a list containing base positions in stems
1 2 3 4 5 6 7 8 9 | ###
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)
plot_stem(data)
|
Loading required package: RRNA
Attaching package: 'RNAstructureModuleMiner'
The following object is masked from 'package:graphics':
stem
pos before after seq pos2 bound
2 14 13 15 A 14 0
21 15 14 16 A 15 -1
1 1 0 2 G 1 13
22 2 1 3 A 2 12
3 3 2 4 C 3 11
4 4 3 5 U 4 10
5 5 4 6 G 5 9
6 6 5 7 G 6 0
7 7 6 8 G 7 0
8 8 7 9 G 8 0
9 9 8 10 C 9 5
10 10 9 11 G 10 4
11 11 10 12 G 11 3
12 12 11 13 U 12 2
13 13 12 14 C 13 1
16 0 -1 1 A 0 14
17 -1 -2 0 A -1 15
[1] "-1 15 0 0 0 1 -1 0"
$x
[1] -1
$y
[1] 0
[1] 1.047198
[1] "14 15 14"
[1] "13 14 13"
[1] "12 13 12"
[1] "11 12 11"
[1] "10 11 10"
[1] "9 10 9"
[1] "New LOOPS: c(5, 9)"
[1] 5
[1] "no sequences to match"
[1] "------------------------------------------------------"
[1] "summary of stems:"
[1] "the number of stems is: 1"
[1] "the bases in stems are: 1 2 3 4 5 9 10 11 12 13"
$`bases in stem 1`
[1] 1 2 3 4 5 9 10 11 12 13
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