Question: Use of clusterProfiler R package
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gravatar for prakashpandey1111
4 months 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 • 180 views
ADD COMMENTlink modified 4 months ago by jared.andrews071.4k • written 4 months ago by prakashpandey11110
1
gravatar for jared.andrews07
4 months ago by
jared.andrews071.4k
St. Louis, MO
jared.andrews071.4k 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 4 months ago by jared.andrews071.4k
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