validateH5ADSCE {zellkonverter} | R Documentation

## Validate H5AD SCE

### Description

Validate a SingleCellExperiment created by `readH5AD()`. Designed to be used inside `testhat::test_that()` during package testing.

### Usage

    validateH5ADSCE(sce, names, missing)

### Arguments

`sce` | A SingleCellExperiment object.
`names` | Named list of expected names. Names are slots and values are vectors of names that are expected to exist in that slot.
`missing` | Named list of known missing names. Names are slots and values are vectors of names that are expected to not exist in that slot.

### Details

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`.

### Value

If checks are successful `TRUE` invisibly, if not other output depending on the context

### Author(s)

Luke Zappia

[Package zellkonverter version 1.4.0 Index]