RUVg_Housekeeping_Normalization: RUVg_Housekeeping_Normalization

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

RUVg_Housekeeping_Normalization

Description

a normalization method that uses residuals from a fitted model to Remove Unwanted Variation by leveraging housekeeping genes (https://www.nature.com/articles/nbt.2931).

Usage

RUVg_Housekeeping_Normalization(
  seuratObj,
  assay = "RNA",
  targetAssayName = "RUVg",
  k = 1
)

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.
targetAssayName	The assay name that the normalized data should be stored in.
k	the number of factors of unwanted variation. See section "Choice of number of factors of unwanted variation." in paper cited in the description.

Value

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

bimberlabinternal/CellMembrane documentation built on Oct. 16, 2024, 6:53 a.m.