Converting assays inheriting `Assay` class only allows assays named `counts`

[jordanc17]

When converting assays from Seurat to SingleCellExperiment, if they're of the Assay type, the conversion function doesn't properly handle assays other than counts. If there's no slot named counts, this will return a matrix with 0 rows or 0 columns and cause the conversion to fail.

convert2anndata/R/extract_counts_matrix.R

Lines 19 to 20 in 550bfb0

	} else if (inherits(assay_object, "Assay")) {
	GetAssayData(assay_object, slot = "counts")

This section should be updated with the if/else logic used for assays of the Assay5 class:

convert2anndata/R/extract_counts_matrix.R

Lines 12 to 18 in 550bfb0

	if (inherits(assay_object, "Assay5")) {
	if ("counts" %in% Layers(assay_object)) {
	GetAssayData(assay_object, layer = "counts")
	} else {
	# If counts layer doesn't exist, try default
	GetAssayData(assay_object)
	}