cluster composition in Mfuzz package
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@thomasdobrenel-9981
Last seen 5.4 years ago

Hello everybody,

I am using the Mfuzz package (v. 2.30.0) for analysing the effect of a time series on gene expression and I therefore manage to cluster the genes from this dataset, based on their expression profiles. I would like to know how it is possible to actually identify which genes are part of each cluster, in order to export these lists and make some gene ontology analysis. Is it possible with a function of this package or should I use another package?

I thank you in advance

Sincerely

Tom

cluster mfuzz gene names • 1.2k views
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Assa Yeroslaviz ★ 1.5k
@assa-yeroslaviz-1597
Last seen 4 weeks ago
Munich, Germany

The function acore() can create a list object with all the clusters and their genes with their gene membership values.

You should run something like that:

acore.list <- acore(CountTable,cl=cl)

temp   = sapply(acore.list,'[[',"NAME")

 

temp is than a list of vectors you can use for any downstream analysis

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Thanks, I will give it a try.

I also found (during this time) that it is possible to extract it by writing the lines below (although the genes are then annotated by numbers and not by their actual names):

write.table(cl$cluster,"C:/Users/Thomas/Desktop/cluster.txt",sep="\t")

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