SNP‐based enrichment analysis for WGCNA modules using an hypergeometric test
1
0
Entering edit mode
6 months ago

Hello everyone

I have 13 clusters of co-expressed genes, obtained form an expression dataset of 6800 genes per 27 samples. Among the 6800 genes used for the netowrk analysis, 168 have a single SNPs (compared to the WT strain). I was wondering if an hypergeometric test can applied to find modules enriched with genes having a SNP:

Number of genes with SNP in the turquoise module 17
Total number of genes in the turquoise module 889
Total number of genes in the network 6800
Total number of genes with SNP 168

phyper(17-1,889,6800,168, lower.tail = TRUE, log.p = FALSE) #edited

Does it make any sense?

Thank you

hypergeometrictest SNPs WGCNA • 458 views
ADD COMMENT
3
Entering edit mode
6 months ago

I think that it is [almost] correct. Take a look at THIS same question on StackOverflow where it would end up being:

phyper(16, 889, 6800 - 889, 168, lower.tail = TRUE, log.p = FALSE)

Note, also, whether it is 16 or 17? Please re-check your question.

Kevin

ADD COMMENT
1
Entering edit mode

Thank you Kevin!

I have edited my question

ADD REPLY

Login before adding your answer.

Traffic: 1874 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