Question: ChIPSeeker - problem with GO enrichment analysis
0
gravatar for julia.keith
2.2 years ago by
julia.keith0 wrote:

Hello,

I would like to use ChIPseeker to get GO and KEGG enrichment analysis of my ChIP data (mouse cells mm9), but I am getting an error I don't know how to fix. I have my peak files as BED files and have been able to sucessfully get them read into the package using rtracklayer. I have also been able to plot the annotation features just fine. When I try to use the function "enrichPathway", the system gives me an error that it's looking for the human annotation data which is a problem since my samples are murine. I have looked at the information available but the arguments aren't listed so I don't know how to correct this.

If someone can help me out, I would be very grateful.

Many thanks, juli

`

library("ChIPseeker")

library(TxDb.Mmusculus.UCSC.mm9.knownGene)

library(biomaRt)

library(rtracklayer)

library(org.Mm.eg.db)

peakAnno.d3TCR.p300 <- annotatePeak(d3TCR.p300, tssRegion = c(-3000, 3000), TxDb = TxDb.Mmusculus.UCSC.mm9.knownGene, annoDb = "org.Mm.eg.db")

gene.d3TCRp300 <- seq2gene(d3TCR.p300, tssRegion = c(-1000, 1000), flankDistance= 3000, TxDb=TxDb.Mmusculus.UCSC.mm9.knownGene, sameStrand = FALSE)

pathway.d3TCRp300 <- enrichPathway(gene.d3TCRp300) Loading required package: org.Hs.eg.db Error in eval(expr, envir, enclos) : object 'org.Hs.eg.db' not found In addition: Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'org.Hs.eg.db' `

chip-seq chipseeker • 1.4k views
ADD COMMENTlink modified 20 months ago by Biostar ♦♦ 20 • written 2.2 years ago by julia.keith0
1
gravatar for Guangchuang Yu
2.2 years ago by
Guangchuang Yu2.1k
China/Hong Kong/The University of Hong Kong
Guangchuang Yu2.1k wrote:
pathway.d3TCRp300 <- enrichPathway(gene.d3TCRp300, organism="mouse")

You need to have org.Mm.eg.db installed.

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by Guangchuang Yu2.1k
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