Error in CID.LoadEdges(data.dir = spring.dir)

[SuFuBel]

Hi, trying to run the package as indicated in the vignette, I found the following message. ERROR: from CID.LoadEdges: edges = /edges.csv does not exist. Error in CID.LoadEdges(data.dir = spring.dir) :

[mathewchamberlain]

Hi SuFuBel,

I assume you ran the SPRING pipeline and found this error? You need to direct the code to the location of the "edges.csv" file. What have you set spring.dir to? Can you provide a more expanded segment of code?

Best,

Mathew

[SuFuBel]

Hi Mathew, thank you for replying so fast.

So far after integration by using Seurat I just did labels_fast <- SignacFast(pbmc[["RNA"]])

If I understand correctly I need to extract the edges, write them as .csv and set spring.dir as that directory?

Thank you again, Abel

From: Mathew Chamberlain @.> Reply-To: mathewchamberlain/SignacX @.> Date: Thursday, September 2, 2021 at 3:18 PM To: mathewchamberlain/SignacX @.> Cc: "Suarez-Fueyo, Abel" @.>, Author @.***> Subject: [EXTERNAL] Re: [mathewchamberlain/SignacX] Error in CID.LoadEdges(data.dir = spring.dir) (#12)

Hi SuFuBel,

I assume you ran the SPRING pipeline and found this error? You need to direct the code to the location of the "edges.csv" file. What have you set spring.dir to? Can you provide a more expanded segment of code?

Best,

Mathew

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/mathewchamberlain/SignacX/issues/12#issuecomment-911983230, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ANMRYATJCOXZLPXBDE62PB3T77EXRANCNFSM5DJY6HHQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

[mathewchamberlain]

No problem. Not exactly: there is no need to write the edges to any file -- that functionality is for python-based workflows for generating KNN edges.

In your case, to run SignacX on a Seurat object, just follow the steps here: https://mathewchamberlain.github.io/SignacX/articles/signac-Seurat_pbmcs.html

Or to summarize them here, you just do:

whatever normalization you choose, and then:

pbmc <- RunPCA(pbmc, verbose = FALSE) pbmc <- RunUMAP(pbmc, dims = 1:30, verbose = FALSE) pbmc <- FindNeighbors(pbmc, dims = 1:30, verbose = FALSE) labels_fast <- SignacFast(pbmc, num.cores = 4) celltypes = GenerateLabels(labels_fast, E = pbmc)

Then you have your cell type + cell state + novel cell type labels. Let me know if this works or not please, thanks.

[SuFuBel]

It worked, I had a typo before, thanks a lot.

From: Mathew Chamberlain @.> Reply-To: mathewchamberlain/SignacX @.> Date: Thursday, September 2, 2021 at 3:38 PM To: mathewchamberlain/SignacX @.> Cc: "Suarez-Fueyo, Abel" @.>, Author @.***> Subject: [EXTERNAL] Re: [mathewchamberlain/SignacX] Error in CID.LoadEdges(data.dir = spring.dir) (#12)

No problem. Not exactly: there is no need to write the edges to any file -- that functionality is for python-based workflows for generating KNN edges.

In your case, to run SignacX on a Seurat object, just follow the steps here: https://mathewchamberlain.github.io/SignacX/articles/signac-Seurat_pbmcs.html

Or to summarize them here, you just do:

whatever normalization you choose, and then:

pbmc <- RunPCA(pbmc, verbose = FALSE) pbmc <- RunUMAP(pbmc, dims = 1:30, verbose = FALSE) pbmc <- FindNeighbors(pbmc, dims = 1:30, verbose = FALSE) labels_fast <- SignacFast(pbmc, num.cores = 4) celltypes = GenerateLabels(labels_fast, E = pbmc)

Then you have your cell type + cell state + novel cell type labels. Let me know if this works or not please, thanks.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/mathewchamberlain/SignacX/issues/12#issuecomment-911996873, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ANMRYAW4DLVF7J74LIMT34DT77HDXANCNFSM5DJY6HHQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

[mathewchamberlain]

Excellent, I'll close this now. Feel free to reach out to discuss results, if of interest. Can be reached at chamberlainphd@gmail.com.