Question: clusterProfiler enricher question
1
gravatar for skenoy
2.8 years ago by
skenoy10
skenoy10 wrote:

I meet a problem when use enricher of clusterProfiler :

my CC background gene number is 9052, print summary(ego), its show BgRatio is 9052, but when i use ego@geneSets to show only 5k, then i use plotGOgraph,the first level of go`s gene number is 5k, not 9052, other levels gene number is right as the same as showing of summary(ego)

  1. i use latest version of clusterProfiler
  2. library(clusterProfiler)
    annot <- read.table("PFC/annot.C", header=F, sep="\t", quote="", colClasses = "character")
    allg <- read.table("Unigene.fa.bgl", header=F, colClasses = "character")
    deg <- read.table("../CK-VS-T.glist", header=F, colClasses = "character")
    g2g <- annot[, c("V1", "V2")]
    g2t <- annot[, c("V1", "V3")]
    ego <- enricher(deg$V1, universe=allg$V1, pAdjustMethod = "none", minGSSize = 1, TERM2GENE= g2g, TERM2NAME = g2t, pvalueCutoff =1, qvalueCutoff =1)
    write.table(summary(ego)[,-6][,-8], "test/test.C.xls", sep="\t", row.names=F, quote=F)
    ego <- enricher(deg$V1, universe=allg$V1, pAdjustMethod = "none", minGSSize = 1, TERM2GENE= g2g, TERM2NAME = g2t, pvalueCutoff =0.05, qvalueCutoff =1)
    ego@ontology = "CC"
    if(length(rownames(summary(ego))) != 0)
    {
    pdf("test/test.C.pdf")
    if(length(rownames(summary(ego))) > 9)
    {
        plotGOgraph(ego)
    }else{
        plotGOgraph(ego, firstSigNodes = length(rownames(summary(ego))))
    }
    dev.off()
    }
clusterprofiler enricher • 1.9k views
ADD COMMENTlink modified 2.8 years ago by Guangchuang Yu2.1k • written 2.8 years ago by skenoy10
1
gravatar for Guangchuang Yu
2.8 years ago by
Guangchuang Yu2.1k
China/Hong Kong/The University of Hong Kong
Guangchuang Yu2.1k wrote:

you did not follow the guide, http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example, to make a reproducible example, and I have no idea of your input, output and plot.

BgRatio is 9052, but when i use ego@geneSets to show only 5k

Here, you did not give enough information either.

BgRatio should be something like M/N, M is the number of genes belong the a specific term and N should be the number of all genes in background.

geneSets is a list of geneSet, while each geneSet contains genes that belong to that term, that is corresponding to M.

It seems here 9052 is N and 5k is M and of course they M << N.

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Guangchuang Yu2.1k

yes, I know BgRatio is format to M/N

9052 is N, the number of geneSets is 5k, are they the same? i think it must be the same, or i use plotGOgraph show the first level of go`s gene number is 5k, not 9052

ADD REPLYlink written 2.8 years ago by skenoy10

pls install the newest release of DOSE, it should solve your issue.

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by Guangchuang Yu2.1k
0
gravatar for Guangchuang Yu
2.8 years ago by
Guangchuang Yu2.1k
China/Hong Kong/The University of Hong Kong
Guangchuang Yu2.1k wrote:

reproducible example, pls, otherwise I can't get your idea.

ADD COMMENTlink written 2.8 years ago by Guangchuang Yu2.1k

Please use ADD REPLY/ADD COMMENT to respond to existing posts. SUBMIT ANSWERS should be reserved for new answers to original question.

ADD REPLYlink written 2.8 years ago by genomax65k

OK. thanks for the info

ADD REPLYlink written 2.8 years ago by Guangchuang Yu2.1k
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