Validate a SingleCellExperiment created by readH5AD(). Designed to be used
inside testhat::test_that() during package testing.
validateH5ADSCE(sce, names, missing)A SingleCellExperiment object.
Named list of expected names. Names are slots and values are vectors of names that are expected to exist in that slot.
Named list of known missing names. Names are slots and values are vectors of names that are expected to not exist in that slot.
If checks are successful TRUE invisibly, if not other output
depending on the context
This function checks that a SingleCellExperiment contains the expected items
in each slot. The main reason for this function is avoid repeating code when
testing multiple .h5ad files. The following items in names and missing
are recognised:
assays - Assay names
colData - colData column names
rowData - rowData column names
metadata - metadata names
redDim - Reduced dimension names
varm - Column names of the varm rowData column (from the AnnData varm
slot)
colPairs - Column pair names
rowPairs - rowData pair names
raw_rowData - rowData columns names in the raw altExp
raw_varm - Column names of the raw varm rowData column (from the
AnnData varm slot)
If an item in names or missing is NULL then it won't be checked. The
items in missing are checked that they explicitly do not exist. This is
mostly for record keeping when something is known to not be converted but can
also be useful when the corresponding names item is NULL.