ClrNormalizeByGroup: ClrNormalizeByGroup

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

ClrNormalizeByGroup

Description

This subsets the input object based on a variable (like dataset), and performs CLR normalization per-group, then combines them

Usage

ClrNormalizeByGroup(
  seuratObj,
  groupingVar,
  assayName = "ADT",
  targetAssayName = NA,
  margin = 1,
  minCellsPerGroup = 20,
  calculatePerFeatureUCell = FALSE,
  featureInclusionList = NULL,
  featureExclusionList = NULL,
  doAsinhTransform = FALSE
)

Arguments

seuratObj	The seurat object
groupingVar	The variable to use to partition the data
assayName	The name of the assay
targetAssayName	If provided, data will be saved to this assay, rather than modifying the source assay
margin	Passed directly to NormalizeData()
minCellsPerGroup	If provided, any group with newer than this many cells will be dropped
calculatePerFeatureUCell	If TRUE, UCell will be run once per feature in the assay
featureInclusionList	If provided, the input assay will be subset to just these features.
featureExclusionList	If provided, the input assay will be subset to exclude these features.
doAsinhTransform	If true, asinh transform will be performed on the raw counts prior to CLR

bimberlabinternal/CellMembrane documentation built on Dec. 20, 2024, 11:13 p.m.