HybridDemultiplexing: HybridDemultiplexing

In LeiLi-Uchicago/HTOreader: An R package for cell hashing demultiplexing

HybridDemultiplexing

Description

function for HybridDemultiplexing

Usage

HybridDemultiplexing(
  object = NULL,
  cellhashing_label = NULL,
  genotype_label = NULL,
  hto_names = NULL,
  c_threshold = 0.7,
  snp_doublet_label = "doublet",
  snp_unassign_label = "unassigned",
  cellhashing_doublet_label = "Doublet",
  cellhashing_negative_label = "Negative",
  pair_info = NULL
)

Arguments

object	Seurat object
cellhashing_label	label name for cell hashing in the meta data
genotype_label	label name for snp-based method in the meta data
hto_names	a vector of all HTO names
c_threshold	threshold of convergence score, default is 0.7.
snp_doublet_label	doublet label in SNP results.
snp_unassign_label	unassigned label in SNP results.
cellhashing_doublet_label	doublet label in cell hashing results.
cellhashing_negative_label	negative label in cell hashing results.
pair_info	Users can provide a list of paired hashtags and genotype groups. For example: pair <- list("Hashtag1" = "singlet0","Hashtag2" = "singlet1","Hashtag3" = "singlet2")

LeiLi-Uchicago/HTOreader documentation built on Aug. 14, 2024, 8:38 p.m.