plot_stem: plot_stem

In RNAstructureModuleMiner: RNA Secondary Structure Comparison and Module Mining

Description

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

Usage

plot_stem(ctFile)

Arguments

ctFile

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

Value

Return a list containing base positions in stems

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)
plot_stem(data)

Example output

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

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