availability Baker dataset

[guidohooiveld]

Hi,
I am exploring your wonderful package, and to check whether the format of input data is OK, I would like to run / compare it with the Baker dataset mentioned in Chapter 5.1 of the online documentation (file: uro.deseq.res.rda).
https://noriakis.github.io/software/ggkegg/usecases.html#visualizing-numerical-attributes-from-deseq2

Could you tell me where I can find this file?

Thanks!

[noriakis]

Thank you for your inquiry and I apologize for the late response. I uploaded the corresponding file in the link below. The link may raise security warnings as it is hosted in our institute at the Human Genome Center. I hope this helps and thank you for using the package. https://w5po.myqnapcloud.com/share.cgi?ssid=fb53d8611b774ce8b48170b44b77503b

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On Wed, Dec 4, 2024 at 4:28 AM Guido Hooiveld ***@***.***> wrote: Hi, I am exploring your wonderful package, and to check whether the format of input data is OK, I would like to run / compare it with the Baker dataset mentioned in Chapter 5.1 of the online documentation (file: uro.deseq.res.rda). https://noriakis.github.io/software/ggkegg/usecases.html#visualizing-numerical-attributes-from-deseq2 Could you tell me where I can find this file? Thanks! — Reply to this email directly, view it on GitHub <#40>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHNHVPZTKN7VDDEPFKDEB2T2DYA43AVCNFSM6AAAAABS6QMJ46VHI2DSMVQWIX3LMV43ASLTON2WKOZSG4YTKOBTGEZTCMY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[guidohooiveld]

Thanks for providing the file!

Yet, using it i run into an error when running the code of Chapter 5.1 (when assigning the values to the nodes).
Any suggestions?

Thanks again!

> library(ggkegg)
> library(DESeq2)
> library(org.Hs.eg.db)
> library(dplyr)
> 
> load("uro.deseq.res.rda") 
> res
class: DESeqDataSet 
dim: 29744 26 
metadata(1): version
assays(8): counts avgTxLength ... replaceCounts replaceCooks
rownames(29744): A1BG A1BG-AS1 ... ZZEF1 ZZZ3
rowData names(27): baseMean baseVar ... maxCooks replace
colnames(26): SRR14509882 SRR14509883 ... SRR14509906 SRR14509907
colData names(27): Assay.Type AvgSpotLen ... viral_infection
  replaceable
> 
> vinf <- results(res, contrast=c("viral_infection","BKPyV (Dunlop) MOI=1","No infection"))
> 
> ## LFC
> g <- pathway("hsa04110") |> mutate(deseq2=assign_deseq2(vinf),
+                                    padj=assign_deseq2(vinf, column="padj"),
+                                    converted_name=convert_id("hsa"))
Error in `mutate()`:
ℹ In argument: `deseq2 = assign_deseq2(vinf)`.
Caused by error in `assign_deseq2()`:
! Please specify Annotation DB to org_db.
Run `rlang::last_trace()` to see where the error occurred.
> 
> ## specifying org_db reults in another error...
> g <- pathway("hsa04110") |> mutate(deseq2=assign_deseq2(vinf, org_db=org.Hs.eg.db),
+                                    padj=assign_deseq2(vinf, column="padj"),
+                                    converted_name=convert_id("hsa"))
Error in `mutate()`:
ℹ In argument: `deseq2 = assign_deseq2(vinf, org_db = org.Hs.eg.db)`.
Caused by error in `AnnotationDbi::mapIds()`:
! argument "column" is missing, with no default
Run `rlang::last_trace()` to see where the error occurred.
> 
>
> packageVersion("ggkegg")
[1] ‘1.4.0’
> 

[noriakis]

Thank you very much for reporting this issue. This is obviously a bug in a newer version involving `mapIds` (I was using `select` in the past version). I just created a patch in the latest `devel` and `main` branch of the repository. Could you use `devtools::install_github("noriakis/ggkegg", force=TRUE)` for testing, please? I apologize for the inconvenience caused. Also, I will update the documentation as soon as possible.

…

On Wed, Jan 29, 2025 at 4:12 AM Guido Hooiveld ***@***.***> wrote: Thanks for providing the file! Yet, using it i run into an error when running the code of Chapter 5.1 (when assigning the values to the nodes). Any suggestions? Thanks again! > library(ggkegg) > library(DESeq2) > library(org.Hs.eg.db) > library(dplyr) > > load("uro.deseq.res.rda") > res class: DESeqDataSet dim: 29744 26 metadata(1): version assays(8): counts avgTxLength ... replaceCounts replaceCooks rownames(29744): A1BG A1BG-AS1 ... ZZEF1 ZZZ3 rowData names(27): baseMean baseVar ... maxCooks replace colnames(26): SRR14509882 SRR14509883 ... SRR14509906 SRR14509907 colData names(27): Assay.Type AvgSpotLen ... viral_infection replaceable > > vinf <- results(res, contrast=c("viral_infection","BKPyV (Dunlop) MOI=1","No infection")) > > ## LFC > g <- pathway("hsa04110") |> mutate(deseq2=assign_deseq2(vinf), + padj=assign_deseq2(vinf, column="padj"), + converted_name=convert_id("hsa")) Error in `mutate()`: ℹ In argument: `deseq2 = assign_deseq2(vinf)`. Caused by error in `assign_deseq2()`: ! Please specify Annotation DB to org_db. Run `rlang::last_trace()` to see where the error occurred. > > ## specifying org_db reults in another error... > g <- pathway("hsa04110") |> mutate(deseq2=assign_deseq2(vinf, org_db=org.Hs.eg.db), + padj=assign_deseq2(vinf, column="padj"), + converted_name=convert_id("hsa")) Error in `mutate()`: ℹ In argument: `deseq2 = assign_deseq2(vinf, org_db = org.Hs.eg.db)`. Caused by error in `AnnotationDbi::mapIds()`: ! argument "column" is missing, with no default Run `rlang::last_trace()` to see where the error occurred. > > > packageVersion("ggkegg") [1] ‘1.4.0’ > — Reply to this email directly, view it on GitHub <#40 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHNHVP4VTEPYHSF6CLF52BD2M7JBNAVCNFSM6AAAAABS6QMJ46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMMJZHA2TCNJRHE> . You are receiving this because you commented.Message ID: ***@***.***>