Is Gex_nUMI supposed to be automatically calculated?

[markphillippebworth]

When I add a GeneExpressionMatrix to an ArchR project, is it supposed to automatically calculate the Gex_nUMI metadata column? I'm running it and realizing its not there. And no error was hit when I tried to run addIterativeLSI within the GeneExpressionMatrix, with the depthCol set to Gex_nUMI. The results were terrible though.

[rcorces]

Gex_nUMI is automatically calculated from your seRNA. If its empty, then there is probably something wrong with your seRNA

ArchR/R/MatrixGeneExpression.R

Line 77 in 968e442

nUMI <- Matrix::colSums(assay(seRNA))

[markphillippebworth]

Late response, but I was able to get it to work. Something odd happened the first time (the gene expression matrix was present, but no metadata summaries added). By adding the gene expression matrix again, I was able to get Gex_nUMI and other columns added to the metadata.