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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.
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.

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Syntax

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,
  ...
)

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Behavior

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

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Migration

# 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")

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See Also