SpatialNormalizeByGroup: SpatialNormalizeByGroup

In bimberlabinternal/CellMembrane: A package with high-level wrappers and pipelines for single-cell RNA-seq tools

SpatialNormalizeByGroup

Description

a wrapper function to iteratively apply normalization methods that may be sensitive to batch variation.

Usage

SpatialNormalizeByGroup(
  seuratObj,
  assay = "RNA",
  normalizationMethod = NULL,
  inferAssayName = T,
  targetAssayName = NULL,
  groupField = "SlideName",
  k = NA
)

Arguments

seuratObj	The Seurat object that holds the data to be normalized.
assay	The assay holding the raw data - the counts slot will be assumed to hold raw data.
normalizationMethod	The normalization method to be applied (One of: Q3, Housekeeping, or RUVg) across the batches/groups in groupField.
inferAssayName	Boolean to determine whether or not the function should infer the name of the assay that the normalized counts will be stored in based on the name of normalizationMethod.
targetAssayName	The assay name that the normalized data should be stored in.
groupField	the metadata column that delineates how the samples within Seurat object should be grouped.
k	a passthrough variable for the RUVg normalization. Please see RUVg_Housekeeping_Normalization for details about this parameter.

Value

Returns a Seurat object containing normalized counts stored in the counts slot of the "Housekeeping" assay.

bimberlabinternal/CellMembrane documentation built on Nov. 15, 2024, 9:34 p.m.