HTOcutoff: HTOcutoff

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

HTOcutoff

Description

function to determine cutoff for HTO signals

Usage

HTOcutoff(
  object = NULL,
  assay = "HTO",
  method = "log",
  min_limit = 1.5,
  re_sampling_cutoff = NULL
)

Arguments

object	Seurat object
assay	the assay name of Hashtag signals, Default is "HTO"
method	normalize method, could be "CLR" or 'log'. Default is "log"
min_limit	min limit of cutoff, default is 1.5 (empirical value)
re_sampling_cutoff	a cutoff for re-sampling when there are too many HTOs (> 4) in a single experiment, by default we set 1.5 for CLR and 3 for log method

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