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Published 20 hours ago • verified publisher icon GreenleafLab

Error in lsiProjection

Open pbrazda opened this issue 4 years ago • 0 comments

Hi ,

I'm having some trouble with the umapProjection from 'Update scRNA_02_Cluster_Disease_w_Reference_v1.R' at line 366: umapProjection <- uwot::umap_transform(as.matrix(lsiProjection$matSVD)[,1:25], umapManifold, verbose = TRUE)

The error is Error in lsiProjection$matSVD : $ operator not defined for this S4 class but I cannot see the matSVD slot here, not even within lsiProjection@ .

As I understand, it should be coming from lsiProjection <- projectLSI(matProjectLSI, lsiReference)

I would like to use it to project a second scRNAseq dataset on a previously determined scRNAseq umap.

Thank you for any comments and tips!

Best, Peter

pbrazda avatar Aug 24 '20 15:08 pbrazda