DOSE

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Saving separate dotplots with for loop

1

hello, I want to create several PDF files with Functional_enrichment Doplot as Chipseeker vignette with a for loop. http://bioconductor.org/packages/devel/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html but the PDF are empty with no pages. If I avoid...

mirkocelii

enricher_internal.R code may have mistake

1

At the 100th line code in [https://github.com/YuLab-SMU/DOSE/blob/master/R/enricher_internal.R](url), it is `numWdrawn=k-1`, it should represent the number of the real terms we get, but why minus one? I think 'minus one' is...

tangmaomao16

bug in DOSE:::gseaScores - Error in if (abs(max.ES) > abs(min.ES))

9

Hi, I am using R v4 and the latest clusterProfiler and DOSE package (DOSE version 3.16.0) and I get the following error: ``` Error in if (abs(max.ES) > abs(min.ES)) {...

therealgenna

Error: object 'upsetplot' not found

1

I'm unable to use 'upsetplot' (either as part of DOSE or clusterProfiler) - why am I receiving this error? DOSE was installed via: `BiocManager::install("DOSE") ` ``` [](> library(DOSE) DOSE v3.12.0...

TimJCooper

Some problems about 'maxGSSize' parameter in enricher_interval series function

1

Hi~ Recently I have realized that there is a more hidden parameters called `maxGSSize`, which really influence the result of enricher/GSEA analysis. According to the raw code in DOSE，I think...

huangwb8

### Prerequisites + [ ] Have you read [Feedback](https://guangchuangyu.github.io/dose/#feedback) and follow the [guide](https://guangchuangyu.github.io/2016/07/how-to-bug-author/)? * [ ] make sure your are using the latest release version * [ ] read the...

ieiwk

Disrepancy GSEA results when using by="DOSE" or by="fgsea"

3

Hi, I don't know whether I should ask here, or at the maintainer of `fgsea` (@assaron), but after analyzing the example DOSE dataset using the GSEA algorithm implemented in either...

guidohooiveld

https://github.com/GuangchuangYu/DOSE/blob/01913f001ad7ea0808a61e30f7f5943a84c3a23f/R/gsea.R#L57 As a user, I would not expect `pvalueCutoff` to be applied to the `p.adjust` column. Or at least I think it should be made clear in the documentation that...

kevinrue

Could you clarify in the documentation for your GSEA algorithm what the difference is between p.adjust and qvalue output? Usually p.adjust is run with 'fdr' as default method which should...

mgandal

Update to DisGeNet 5?

2

I am under the impression that the DGN database included with the package corresponds to DisGeNet release 4. Would it be possible to upgrade it to version 5? There is...

tonigi