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Question: custom background list for ReactomePA
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gravatar for andrew.gehrke
11 months ago by
andrew.gehrke0 wrote:

Hi Guangchuang,

Is there a way to create a custom universe for the enrichPathway function?  I am using a non-model organism and want to use only the human genes that my organism possesses as the background.  In general im not sure how to use the universe flag, could you provide any help here?

Thanks for your time,

-Andrew

ADD COMMENTlink modified 11 months ago • written 11 months ago by andrew.gehrke0

The universe is the genes of the background so you can pass a vector like c("G1", "G2", "G3", ...) enrichPathway will use it.

ADD REPLYlink written 11 months ago by Lluís Revilla Sancho430
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gravatar for andrew.gehrke
11 months ago by
andrew.gehrke0 wrote:

Thanks for the response Lluis.  Just so im clear, it should work with this?

pathway2 <- enrichPathway(gene, universe = c("G1", "G2", "G3"))

It seems like no matter what I put in the universe section I always get an error that says 

No gene set have size > 10 ...
--> return NULL...

Do you have a suggestion for importing the gene set from a txt list that I have?  Ive tried all different ways to important and still cant seem to get it.  

Thank you!

-Andrew

 

ADD COMMENTlink written 11 months ago by andrew.gehrke0

That means that you are filtering by size of the gene sets and that they are smaller than 10 genes. Without knowing the specific format I can't provide advice. Could you ask a new question with the file (or part of it) describing the format and what have you tried to import it?

ADD REPLYlink written 11 months ago by Lluís Revilla Sancho430
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