plot_bulge: plot_bulge

In RNAstructureModuleMiner: RNA Secondary Structure Comparison and Module Mining

Description

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

Usage

plot_bulge(ctFile)

Arguments

ctFile

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

Value

Return a list containing base positions in bulge loops

Examples

###
col1 <- c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19)
col2 <- c("G","C","C","A","C","C","C","U","G","C","A","G","G","G","U","C","G","G","C")
col3 <- c(0,1,2,3,4,5,6,7,8,0,10,11,12,13,14,15,16,17,18)
col4 <- c(2,3,4,5,6,7,8,9,0,11,12,13,14,15,16,17,18,19,0)
col5 <- c(19,18,17,15,14,13,12,11,10,9,8,7,6,5,4,0,3,2,1)
col6 <- c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19)
data <- matrix(c(col1,col2,col3,col4,col5,col6),byrow=FALSE,ncol =6)
plot_bulge(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   20     19    21   A   20     0
21  21     20    22   A   21    -1
1    1      0     2   G    1    19
24   2      1     3   C    2    18
3    3      2     4   C    3    17
4    4      3     5   A    4    15
5    5      4     6   C    5    14
6    6      5     7   C    6    13
7    7      6     8   C    7    12
8    8      7     9   U    8    11
9    9      8    10   G    9    10
10  10      9    11   C   10     9
11  11     10    12   A   11     8
12  12     11    13   G   12     7
13  13     12    14   G   13     6
14  14     13    15   G   14     5
15  15     14    16   U   15     4
16  16     15    17   C   16     0
17  17     16    18   G   17     3
18  18     17    19   G   18     2
19  19     18    20   C   19     1
22   0     -1     1   A    0    20
23  -1     -2     0   A   -1    21
[1] "-1 21 0 0 0 1 -1 0"
$x
[1] -1

$y
[1] 0

[1] 1.047198
[1] "20 21 20"
[1] "19 20 19"
[1] "18 19 18"
[1] "17 18 17"
[1] "15 17 16"
[1] "New LOOPS:  c(3, 17)"
[1] 3
[1] "4 15 4.95105651629515 -0.309016994374947 5.53884176858763 0.5 4 2.44929359829471e-16"
$x
[1] -0.9510565

$y
[1] 0.309017

[1] 1.075232
[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] "8 9 8"
[1] "7 8 7"
[1] "6 7 6"
[1] "5 6 5"
[1] "4 5 4"
[1] "New LOOPS:  c(15, 4)"
[1] 15
[1] "17 3 4 1 4 2.44929359829471e-16 4.95105651629515 1.30901699437495"
[2] "17 3 4 1 4 6.66133814775094e-16 4.95105651629515 1.30901699437495"
$x
[1] 0.9510565 0.9510565

$y
[1] 0.309017 0.309017

[1] 1.075232 1.075232
[1] "2 3 2"
[1] "1 2 1"
[1] "New LOOPS:  c(19, 1)"
[1] 19
[1] "no sequences to match"
[1] "------------------------------------------------------"
[1] "summary of bulge loops:"
[1] "the number of bulge loops is: 1"
[1] "the bases in bulge loops are: 16"
$`bases in bulge loop  1`
[1] 16

There were 50 or more warnings (use warnings() to see the first 50)

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