Question: R package to perform functional enrichment of clustered human gene data
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gravatar for prakashpandey1111
7 days ago by
prakashpandey11110 wrote:

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

R • 122 views
ADD COMMENTlink modified 5 days ago by doctor.dee00560 • written 7 days ago by prakashpandey11110

Gene data means RNA-seq?

ADD REPLYlink written 7 days ago by ATpoint5.5k

You can have a look at ChIPpeakAnno. All you need is just gene location i.e. bed file containing chromosome genestart geneend.

ADD REPLYlink written 6 days ago by nitinnarwade1504170
1
gravatar for doctor.dee005
5 days ago by
Bioinformatics Center, Pune
doctor.dee00560 wrote:

have a look on clusterProfiler

ADD COMMENTlink written 5 days ago by doctor.dee00560

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.

ADD REPLYlink modified 1 day ago • written 1 day ago by prakashpandey11110

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))

ADD REPLYlink written 1 day ago by prakashpandey11110

"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")

ADD REPLYlink written 1 day ago by prakashpandey11110
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