> ## Documentation Index
> Fetch the complete documentation index at: https://mintlify.com/satijalab/seurat-wrappers/llms.txt
> Use this file to discover all available pages before exploring further.

# RunQuantileAlignSNF()

> Deprecated — calls RunQuantileNorm() internally

<Warning>
  `RunQuantileAlignSNF()` is **deprecated**. It now redirects to `RunQuantileNorm()` internally. Use `RunQuantileNorm()` directly in all new code.
</Warning>

`RunQuantileAlignSNF()` was the original LIGER quantile alignment function. It is kept for backward compatibility but calls `RunQuantileNorm()` with a compatible subset of parameters. Not all parameters from the old API are forwarded.

## Syntax

```r theme={null}
RunQuantileAlignSNF(
  object,
  split.by = "orig.ident",
  reduction = "iNMF_raw",
  reduction.name = "iNMF",
  reduction.key = "iNMF_",
  recalc.snf = FALSE,
  ref_dataset = NULL,
  prune.thresh = 0.2,
  min_cells = 2,
  quantiles = 50,
  nstart = 10,
  resolution = 1,
  center = FALSE,
  id.number = NULL,
  print.mod = FALSE,
  print.align.summary = FALSE,
  ...
)
```

## Behavior

Calling `RunQuantileAlignSNF()` emits a deprecation message and immediately delegates to `RunQuantileNorm()` with the following parameter mappings:

| RunQuantileAlignSNF | RunQuantileNorm  |
| ------------------- | ---------------- |
| `split.by`          | `split.by`       |
| `reduction`         | `reduction`      |
| `reduction.name`    | `reduction.name` |
| `reduction.key`     | `reduction.key`  |
| `quantiles`         | `quantiles`      |

Other parameters (`recalc.snf`, `prune.thresh`, `nstart`, `resolution`, `id.number`, `print.mod`, `print.align.summary`) are not forwarded.

## Migration

Replace all calls to `RunQuantileAlignSNF()` with `RunQuantileNorm()`:

```r theme={null}
# Old (deprecated)
object <- RunQuantileAlignSNF(object, split.by = "orig.ident")

# New
object <- RunQuantileNorm(object, split.by = "orig.ident")
```

## See Also

* [`RunQuantileNorm()`](/api/run-quantile-norm) — Current quantile normalization function
* [`RunSNF()`](/api/run-snf) — Also deprecated
* [LIGER method guide](/methods/liger)