I want to perform functional enrichment for my clustered data. Please suggest me R package so that i can implement it on my clustered data
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prakashpandey1111 •
have a look on clusterProfiler
I performed fuzzy c means using Mfuzz & now i'm confused with the compareCluster function of clusterProfiler package. How to input my Mfuzz result to compareCluster? i performed fuzzy c means using Mfuzz for my expression of 91 uniprot accession numbers across three time points.
datanew<-read.csv("C:/Users/sony/Downloads/new for clust.txt",as.is = TRUE,header = TRUE,sep = "\t",row.names = 1)
logData<-log2(datanew)
eset<- new("ExpressionSet", exprs=as.matrix(logData))
esetS <- standardise(eset)
cl <- mfuzz(esetS,c=4,m=2)
mfuzz.plot(esetS,cl=cl,mfrow=c(2,2))
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written
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prakashpandey1111 •
"gcSample" for geneCluster(from guide) used here is of different type(list) having entrezid's along with their cluster whereas i have accession numbers along with their cluster(cl$cluster).How to make my clustered data suitable for input?
ck <- compareCluster(geneCluster = gcSample, fun = "enrichKEGG")
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Gene data means RNA-seq?
You can have a look at ChIPpeakAnno. All you need is just gene location i.e. bed file containing chromosome genestart geneend.