Question: Use of clusterProfiler R package
gravatar for prakashpandey1111
9 days ago by
prakashpandey11110 wrote:

I want to know what input type compareCluster supports? I performed fuzzy c-means clustering using Mfuzz & now i want to calculate enriched functional categories of each gene clusters.My initial data for clustering was of 91 uniprot ids across three time points.I did this after clustering to have uniprot ids & their cluster belonging-

dat <- data.frame(cl$cluster) colnames(dat)<-c("CLUSTER") write.csv(file="mfuzz.clusters.csv",dat,row.names=TRUE)

Example here which is from vignette - data(gcSample) ck <- compareCluster(geneCluster = gcSample, fun = "enrichKEGG") plot(ck)

functional enrichment • 93 views
ADD COMMENTlink modified 8 days ago by jared.andrews07750 • written 9 days ago by prakashpandey11110
gravatar for jared.andrews07
8 days ago by
Washington University in St. Louis
jared.andrews07750 wrote:

The documentation tells you pretty much exactly what it takes for input. You can pass it a bunch of named lists with the genes for each cluster and it will use that. Or you can use the formula approach as described. I really have no idea what your dataframe looks like without a few lines of example code, so it's tough to help you further.

ADD COMMENTlink written 8 days ago by jared.andrews07750
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