Clustering of gene co-expression network using igraph R package
1
1
Entering edit mode
2.6 years ago

I have a gene co-expression network obtained from RNA-seq data which has more than 10000 nodes and more than 10 lakh edges. I need to cluster this network. Can anyone please suggest a method to cluster this effectively.

I tried with igraph R package, in igraph package many clustering methods are there. How can I identify which is the appropriate method for large gene co-expression network.

R PACKAGE Igraph network clustering gene network • 1.7k views
ADD COMMENT
1
Entering edit mode
ADD REPLY
0
Entering edit mode

Thank you for the guidance

ADD REPLY
1
Entering edit mode
2.6 years ago

There's no right answer to the question of which clustering method is appropriate. You need first to define what appropriate is in your context and second, how you are going to evaluate the outcome. With clustering one may need to explore different approaches as outcome is dependent on what structure is present in the data and on what one expects/wants to see (subject to other constraints such as being able to compute when the data is big).

ADD COMMENT

Login before adding your answer.

Traffic: 1979 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6