CiteSeqDimRedux.PCA: Perform DimRedux on CiteSeq using PCA input

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

Perform DimRedux on CiteSeq using PCA input

Description

Perform DimRedux on CiteSeq

Usage

CiteSeqDimRedux.PCA(
  seuratObj,
  assayName = "ADT",
  print.plots = TRUE,
  performClrNormalization = TRUE,
  doUMAP = TRUE,
  dimsToUse = NULL,
  adtWhitelist = NULL,
  adtBlacklist = NULL
)

Arguments

seuratObj	The seurat object
assayName	The name of the assay holding the ADT data.
print.plots	If true, QC plots will be printed
performClrNormalization	If true, Seurat's CLR normalization will be performed. Otherwise this expected data to be pre-normalized
doUMAP	If true, RunUMAP will be performed
dimsToUse	An optional vector of PCs to use in tSNE/UMAP
adtWhitelist	An optional vector of ADTs that will be included in PCA. If NULL, all will be used.
adtBlacklist	An optional vector of ADTs that will be excluded from PCA. If NULL, all will be used.

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