RunQuantileAlignSNF: Run quantileAlignSNF on a Seurat object

In satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat Object

Run quantileAlignSNF on a Seurat object

Description

This is a deprecated function. Call 'RunQuantileNorm' instead.

Usage

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,
  ...
)

Arguments

object	A merged Seurat object
split.by	Attribute for splitting, defaults to "orig.ident"
reduction	Name of reduction to use
reduction.name	Name to store resulting DimReduc object as
reduction.key	Key for resulting DimReduc
recalc.snf	Recalculate SNF
ref_dataset	Name of dataset to use as a "reference" for normalization. By default, the dataset with the largest number of cells is used.
prune.thresh	Minimum allowed edge weight. Any edges below this are removed (given weight 0) (default 0.2)
min_cells	Minimum number of cells to consider a cluster shared across datasets (default 2)
quantiles	Number of quantiles to use for quantile normalization (default 50).
nstart	Number of times to perform Louvain community detection with different random starts (default 10).
resolution	Controls the number of communities detected. Higher resolution -> more communities. (default 1)
center	Centers the data when scaling factors (useful for less sparse modalities like methylation data). (default FALSE)
id.number	Number to use for identifying edge file (when running in parallel) (generates random value by default).
print.mod	Print modularity output from clustering algorithm (default FALSE).
print.align.summary	Print summary of clusters which did not align normally (default FALSE).
...	Arguments passed to other methods, and to SNF if recalc.snf = TRUE or SNF hasn't been run

Value

A Seurat object with embeddings from quantileAlignSNF stored as a DimReduc object with name reduction.name (key set to reduction.key)

See Also

RunQuantileNorm

satijalab/seurat-wrappers documentation built on April 10, 2024, 3:25 p.m.