Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘assay’ for signature ‘"dgRMatrix", "character"’

[houruiyan]

Hello, thank you for your effort to develop this good tools.

I meet some trouble when I use it.
My kcadata is a sce data type.

But when I run clusters <- quickCluster(kcadata@assays@data$X) It can run smoothly.

However, when I run computeSumFactors, It has another new question. Hope to get your help. Thank you!

[LTLA]

For quickCluster, it's expecting an assay called counts. If your count data is differently named, specify it in assay.type.

Same for your first error using computeSumFactors.

For the second error, all compute*Factors functions expect an SCE input. If you have a matrix, use scran::calculateSumFactors instead - see the documentation for more details.