RNAstrCluster: A function for RNAs clustering by their structure similarites

Description Usage Arguments Value Author(s) Examples

View source: R/RNAstrCluster.R

Description

Given a RNA secondary structure,it compute simility of these RNAs and cluster them

Usage

1
RNAstrCluster(ctFiles)

Arguments

ctFiles

A list contain RNA structures needed to cluster

Value

Return simility matrix and cluster tree

Author(s)

Zheng Hewei

Examples

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Example output

Loading required package: RRNA

Attaching package: 'RNAsmc'

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

    stem

[1] "RNAs being compared:"
[1] "RNA a: 1 RNA b: 1"
[1] "RNAs being compared:"
[1] "RNA a: 1 RNA b: 2"
[1] "RNAs being compared:"
[1] "RNA a: 1 RNA b: 3"
[1] "RNAs being compared:"
[1] "RNA a: 1 RNA b: 4"
[1] "RNAs being compared:"
[1] "RNA a: 2 RNA b: 1"
[1] "RNAs being compared:"
[1] "RNA a: 2 RNA b: 2"
[1] "RNAs being compared:"
[1] "RNA a: 2 RNA b: 3"
[1] "RNAs being compared:"
[1] "RNA a: 2 RNA b: 4"
[1] "RNAs being compared:"
[1] "RNA a: 3 RNA b: 1"
[1] "RNAs being compared:"
[1] "RNA a: 3 RNA b: 2"
[1] "RNAs being compared:"
[1] "RNA a: 3 RNA b: 3"
[1] "RNAs being compared:"
[1] "RNA a: 3 RNA b: 4"
[1] "RNAs being compared:"
[1] "RNA a: 4 RNA b: 1"
[1] "RNAs being compared:"
[1] "RNA a: 4 RNA b: 2"
[1] "RNAs being compared:"
[1] "RNA a: 4 RNA b: 3"
[1] "RNAs being compared:"
[1] "RNA a: 4 RNA b: 4"
$simility_mat
          str1      str2      str3      str4
str1 10.000000  9.564912  3.959524 10.000000
str2  9.564912 10.000000  3.959524  9.564912
str3  3.959524  3.959524 10.000000  3.959524
str4 10.000000  9.564912  3.959524 10.000000

$cluster_tree

Call:
stats::hclust(d = d_mat)

Cluster method   : complete 
Distance         : euclidean 
Number of objects: 4 

RNAsmc documentation built on March 19, 2018, 9:03 a.m.

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