sce_norm: Normalize counts either by 'scran' or 'sctransform'.

In bioinfocz/scdrake: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

Normalize counts either by scran or sctransform.

Description

Normalize counts either by scran or sctransform.

Usage

sce_norm_fn(sce_cc, norm_type = c("scran", "sctransform", "none"), ...)

scran_normalization(
  sce,
  use_quickcluster = TRUE,
  quickcluster_method = c("igraph", "hclust"),
  BSPARAM = BiocSingular::IrlbaParam(),
  BPPARAM = BiocParallel::SerialParam(),
  ...
)

sctransform_normalization(
  sce,
  vars_to_regress = NULL,
  n_hvg = 3000L,
  method = "glmGamPoi",
  seed = 1L,
  verbose = TRUE,
  ...
)

Arguments

sce_cc	(input target) A SingleCellExperiment object.
norm_type	A character scalar: type of normalization.
...	Passed to scran_normalization() or sctransform_normalization().
sce	A SingleCellExperiment object.
use_quickcluster	A logical scalar: if TRUE, do scran::quickCluster() prior to normalization.
quickcluster_method	A character scalar: clustering method: "igraph" uses graph-based clustering "hclust" uses hierarchical clustering See ?scran::quickCluster for more details.
BSPARAM	A BiocSingular::BiocSingularParam object.
BPPARAM	A BiocParallel::BiocParallelParam object.
vars_to_regress	A list of character scalars: which variables to regress out during normalization. Passed to Seurat::SCTransform().
n_hvg	An integer scalar: number of HVGs to take. Passed to Seurat::SCTransform().
method	A character scalar: passed to Seurat::SCTransform().
seed	An integer scalar: passed to Seurat::SCTransform().
verbose	A logical scalar: passed to Seurat::SCTransform().

Value

A SingleCellExperiment object. normalization_type = norm_type is appended to metadata() of the returned SingleCellExperiment object. Output target: sce_norm

The following items are added to metadata() of the returned SingleCellExperiment object:

• normalization_type: value of the norm_type function argument.

• For norm_type = "sctransform": sctransform_hvg_ids, sctransform_pearson_residuals, sctransform_vst.out, sctransform_model_list.

sctransform_normalization()

Seurat::SCTransform() is returning counts in log1p (natural log) scale, but these are transformed to log2.

bioinfocz/scdrake documentation built on Sept. 19, 2024, 4:43 p.m.