> ## 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.

# RunSNF()

> Deprecated — use RunQuantileNorm() instead

<Warning>
  `RunSNF()` is **deprecated**. The function body is disabled and it emits a `.Deprecated()` call redirecting users to `RunQuantileNorm()`. Do not use this function in new code.
</Warning>

`RunSNF()` was used to generate a shared factor neighborhood graph as part of the original LIGER integration pipeline. It has been fully replaced by `RunQuantileNorm()`, which combines quantile alignment and produces the final integrated embedding in a single step.

## Syntax

```r theme={null}
RunSNF(
  object,
  split.by = "orig.ident",
  reduction = "iNMF_raw",
  dims.use = NULL,
  dist.use = "CR",
  center = FALSE,
  knn_k = 20,
  k2 = 500,
  small.clust.thresh = knn_k,
  ...
)
```

## Behavior

Calling `RunSNF()` triggers `.Deprecated(new = 'RunQuantileNorm')` and does not perform any computation. The function returns invisibly after emitting the deprecation warning.

## Migration

```r theme={null}
# Old (deprecated — no longer functional)
object <- RunSNF(object, split.by = "orig.ident")
object <- RunQuantileAlignSNF(object, split.by = "orig.ident")

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

## See Also

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