How to: Custom SingleCellExperiment Object

[eden528]

Hi, I am trying to use this with a non-10X count matrix and 10X Visium barcodes. How can I generate the SingleCellExperiment object using my count matrix (standard format) and the Visium barcodes + coordinates file?

Thank you!

[edward130603]

See the SCE and SummarizedExperiment manual pages for info on how to create the object:
https://rdrr.io/bioc/SingleCellExperiment/man/SingleCellExperiment.html
https://www.rdocumentation.org/packages/SummarizedExperiment/versions/1.2.3/topics/RangedSummarizedExperiment-class

You can add the count matrix (genes * spots) to the counts slot within assays, and the coordinates can be stored within colData.

Example:

mySCE = SingleCellExperiment(assays=list(counts=myCountsMatrix), colData = cbind(myXcoordinates, myYcoordinates))