createNet | R Documentation |

From an expression matrix, this function creates a co-expression network like a graph object using a threshold value and one similarity function.

createNet(expData, method, threshold)

`expData` |
A whole expression matrix or differentially expressed genes matrix, it may be stored in a SummarizedExperiment object. |

`method` |
A function to calculate the similarity matrix between genes. It can be "correlation" to use Pearson function or "mutual information" to use a based on entropy information function. |

`threshold` |
A value between 0 and 1 to filter the similarity matrix and create the co-expression network. |

An undirected co-expression network as igraph object.

Juan David Henao Sanchez <judhenaosa@unal.edu.co>

Liliana Lopez Kleine <llopezk@unal.edu.co>

`findThreshold`

to obtain a threshold value based on biology network assumptions.

# Loading data pathfile <- system.file("extdata","expression_example.txt",package = "coexnet") data <- read.table(pathfile,stringsAsFactors = FALSE) # Building the network cor_pearson <- createNet(expData = data,threshold = 0.7,method = "correlation") cor_pearson mut_inf <- createNet(expData = data,threshold = 0.5,method = "mutual information") mut_inf

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.