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Question: ClusterProfiler: Input file from methylation data in GO Classification (groupGO)
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gravatar for WF
5 weeks ago by
WF0
WF0 wrote:

Dear all,

Good day to you all. I'm dealing with methylation data and having hyper and hypo methylation annot. symbol from package annotatr and now would like to perform GO and KEGG analysis using clusterProfiler package.

I have tried out to run hyper methylation annot. sympol using (1) only annotation symbol (gene list) (2) annotation symbol (gene list) and methylation difference, but shown with no count, no GeneRatio and no gene ID but just a list... as shown below

>>>>

"ID" "Description" "Count" "GeneRatio" "geneID"
"GO:0005886" "GO:0005886" "plasma membrane" 0 "0/0" ""
"GO:0005628" "GO:0005628" "prospore membrane" 0 "0/0" ""
"GO:0005789" "GO:0005789" "endoplasmic reticulum membrane" 0 "0/0" ""
"GO:0019867" "GO:0019867" "outer membrane" 0 "0/0" ""
"GO:0031090" "GO:0031090" "organelle membrane" 0 "0/0" ""
"GO:0034357" "GO:0034357" "photosynthetic membrane" 0 "0/0" ""
"GO:0036362" "GO:0036362" "ascus membrane" 0 "0/0" ""

<<<<

Anyone can please advise what information needed to improve? As per from example of clusterProfiler, it uses "geneList from package DOSE" and I could not view what kind of data deposited inside. I ran the example shown in tutorial and it works well as below in my system:

>>>>
"ID" "Description" "Count" "GeneRatio" "geneID"
"GO:0005886" "GO:0005886" "plasma membrane" 54 "54/207" "S100A9/MELK/S100A8/MARCO/ASPM/CXCL10/LAMP3/CEP55/UGT8/UBE2C/SLC7A5/CXCL9/FADS2/MSLN/IL1R2/KIF18A/S100P/GZMB/TRAT1/GABRP/AQP9/GPR19/SLC2A6/KIF20A/LAG3/NUDT1/CACNA1D/VSTM4/ITPR1/SYT17/SLC16A4/CORIN/KCNK15/CA12/KCNE4/HLA-DQA1/ADH1B/PDZK1/C7/ACKR1/COL17A1/PSD3/EMCN/SLC44A4/LRP2/NLGN4X/MAPT/ERBB4/CX3CR1/LAMP5/ABCA8/STEAP4/PTPRT/CYBRD1"
"GO:0005628" "GO:0005628" "prospore membrane" 0 "0/207" ""
"GO:0005789" "GO:0005789" "endoplasmic reticulum membrane" 8 "8/207" "FADS2/CDK1/CHODL/ITPR1/HLA-DQA1/CYP4F8/CYP4B1/FMO5"
"GO:0019867" "GO:0019867" "outer membrane" 3 "3/207" "BCL2A1/MAOB/PGR"

<<<<

Thank you very much for your favourable reply.

Best wishes,

WF

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