Update Scissor.R with 'data' Layer for Seurat V5

[yifanfu01]

Hi sunduanchen, Due to the upgrade of Seurat, the way to get data matrix has changed. Guys met error:

infos1 <- Scissor(bulk_dataset, sc_dataset, phenotype, alpha = 0.05, family = "cox", Save_file = 'Scissor_LUAD_survival.RData')
Error in as.matrix(sc_dataset@assays$RNA@data) :
no slot of name"data" for this object of class "Assay5"

as mentioned in #59 Here, I fixed the problem and hope it will help.

[sunduanchen]

Thanks a bunch.

Best, Duanchen

On Sat, 11 May 2024 at 02:01, Jacob Yifan FU @.***> wrote:

Hi sunduanchen, Due to the upgrade of Seurat, the way to get data matrix has changed. Here, I fixed the problem and hope it will help.

You can view, comment on, or merge this pull request online at:

https://github.com/sunduanchen/Scissor/pull/62 Commit Summary

• dee4a2e https://github.com/sunduanchen/Scissor/pull/62/commits/dee4a2eb6302b16900774422ae9278eae93d234a Update Scissor.R with 'data' Layer

File Changes

(1 file https://github.com/sunduanchen/Scissor/pull/62/files)

• M R/Scissor.R https://github.com/sunduanchen/Scissor/pull/62/files#diff-98f95c53a59405f9354e763ffc5d5bcc4ece25c9cc1d91996f6fd3a3706ae407 (2)

Patch Links:

• https://github.com/sunduanchen/Scissor/pull/62.patch
• https://github.com/sunduanchen/Scissor/pull/62.diff

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