Question: R package to perform functional enrichment of clustered human gene data
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gravatar for prakashpandey1111
10 weeks 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 • 193 views
ADD COMMENTlink modified 10 weeks ago by doctor.dee005130 • written 10 weeks ago by prakashpandey11110

Gene data means RNA-seq?

ADD REPLYlink written 10 weeks ago by ATpoint7.5k

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 10 weeks ago by nitinnarwade1504200
1
gravatar for doctor.dee005
10 weeks ago by
doctor.dee005130
Bioinformatics Center, Pune
doctor.dee005130 wrote:

have a look on clusterProfiler

ADD COMMENTlink written 10 weeks ago by doctor.dee005130

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 9 weeks ago • written 9 weeks 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 modified 7 weeks ago by Ram17k • written 9 weeks 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 modified 7 weeks ago by Ram17k • written 9 weeks ago by prakashpandey11110
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