ceRNAnetsim
ceRNAnetsim helps to understanding complex miRNA:target interactions with the network based approach. It utilizes the amounts of miRNAs and their targets and interaction parameters optionally.
Installation
Installation of ceRNAnetsim:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ceRNAnetsim")
library(ceRNAnetsim)Example
data("minsamp")
minsamp
priming_graph(minsamp,
competing_count = Competing_expression,
miRNA_count = miRNA_expression)
Local Files
The ceRNAnetsim provides various datasets for experimenting with package functions. These are:
- minsamp : the minimum sample consists of 2 miRNAs and 6 genes which are targeted by them. new_counts is a helper dataset for minsamp.
- midsamp : middle-sized sample is a network of 4 miRNAs and 20 competing target genes.
-
huge_example : this dataset is comprised of a large network which incorporates three datasets:
- gene expression levels (RNA-Seq) retrieved from TCGA-BRCA breast cancer
- miRNA expression of a breast cancer patient (from TCGA)
- and the miRNA:target dataset gathered from two different high-throughput experimental studies. (CLASH & CLEAR-CLiP methods)
- The remaining datasets are used as reproducible example of methods shown as Mirtarbase example
Vignettes
The repository of ceRNAnetsim contents the vignettes that follow:
- What does ceRNAnetsim do?
- How to calculate proper number of iterations for simulation of the network
- How does the system do in a real-world network?
- Helper functions for users.
Also see package webpage
