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RunQuantileAlignSNF() is deprecated. It now redirects to RunQuantileNorm() internally. Use RunQuantileNorm() directly in all new code.
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.

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Syntax

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,
  ...
)

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Behavior

Calling RunQuantileAlignSNF() emits a deprecation message and immediately delegates to RunQuantileNorm() with the following parameter mappings:
RunQuantileAlignSNFRunQuantileNorm
split.bysplit.by
reductionreduction
reduction.namereduction.name
reduction.keyreduction.key
quantilesquantiles
Other parameters (recalc.snf, prune.thresh, nstart, resolution, id.number, print.mod, print.align.summary) are not forwarded.

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Migration

Replace all calls to RunQuantileAlignSNF() with RunQuantileNorm(): 
# Old (deprecated)
object <- RunQuantileAlignSNF(object, split.by = "orig.ident")

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

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See Also