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sunduanchen / Scissor

Scissor package
GNU General Public License v3.0
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limma cameraPR #47

Open Able-Andy opened 1 year ago

Able-Andy commented 1 year ago

Hi guy, how to use CAMERA (function name: cameraPR) in the limma R package (v3.42.2) in the Pathway enrichment analysis?

sunduanchen commented 1 year ago

Hi

You can download the pathway gmt files from MSigDB and creat your own signature. Using the following code to run CAMERA.

hg_v6 <- readRDS(paste(rds_paths, gene_sets[i], sep = '/')) index <- ids2indices(hg_v6, DEG_result$Gene) camera <- cameraPR(signature, index)

Best, DS

On Tue, 21 Mar 2023 at 20:51, Able-Andy @.***> wrote:

Hi guy, how to use CAMERA54 (function name: cameraPR) in the limma R package (v3.42.2) in the Pathway enrichment analysis?

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Able-Andy commented 1 year ago

Could you please give me an example of the signature， index ，DEG_result$Gene？