Network Analysis application in Genetic Studies

Background

SNPs are DNA sequence variations in a population. For example DNA molecule 1 has C-G pair of alleles and DNA molecule 2 has T-A pair of alleles as shown below.

"Dna-SNP" by David Hall (Gringer) - Own work. Licensed under CC BY 2.5 via Wikimedia Commons.

In human genome there are around 3 billion base pairs like as we can see above. Variations in these affect traits like eye color, height and disorders like obesity, diabetes etc.

Create network with igraph in 4 simple steps

Lets say, we have a data-frame with node-node-edge values as following,

Now we will build a network based on this data.

Step 1: Load the data and do basic validity checks.

Introduction to Network Analysis terminology

Part of the Network

Node: Nodes are the entities in graph. Eg. If we consider Facebook friends as a graph then every friend is a node.

Edge: These are the relationships between between nodes. Eg. If we consider Facebook friends as a graph then every friendship is an edge.

Types of the Network

Undirected vs Directed

Undirected graph: When the relationship of edge is always valid in both directions then it is called undirected graph. If Dave is friend with Raj on Facebook then Raj is also friend with Dave.