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Quesion on cellTypes_test #9

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alhadjil opened this issue Jul 30, 2021 · 0 comments
Open

Quesion on cellTypes_test #9

alhadjil opened this issue Jul 30, 2021 · 0 comments

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@alhadjil
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alhadjil commented Jul 30, 2021

Hi,

I want to use my scRNAseq dataset using a pretrained model.
https://sydneybiox.github.io/scClassify/articles/pretrainedModel.html

pred_res <- predict_scClassify(exprsMat_test = exprsMat_wang_subset,
                               trainRes = trainClassExample_xin,
                               cellTypes_test = wang_cellTypes,
                               algorithm = "WKNN",
                               features = c("limma"),
                               similarity = c("pearson", "spearman"),
                               prob_threshold = 0.7,
                               verbose = TRUE)

In the vignette the wang_cellTypes where extracted from a preexisting dataset, but my scRNAseq doesn't have any assigned celltypes. How would you proceed with this?

Thanks

@alhadjil alhadjil changed the title How to proceed after prediction is done - UMAP interation Quesion on cellTypes_test Jul 30, 2021
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