classifyCell.by.sigGene: classify cells using signature genes

In Japrin/sscClust: simpler single cell RNAseq data clustering

classify cells using signature genes

Description

classify cells using signature genes

Usage

classifyCell.by.sigGene(
  obj.list,
  gene.core.tb,
  pca.rotation = NULL,
  assay.name = "exprs",
  out.prefix = NULL,
  adjB = NULL,
  meta.cluster = NULL,
  method = "posFreq",
  gene.pos.tb = NULL,
  gene.neg.tb = NULL,
  meta.info.tb = NULL,
  meta.train.tb = NULL,
  ndownsample = 1500,
  myseed = 123456,
  verbose = F,
  sig.prevelance = 0.65,
  ntop = 10,
  ncores = 16,
  bin.z.pos.th = 0.3,
  bin.z.neg.th = 0.3,
  prob.th = 0.8,
  TH.gene.exp.freq = 0.65,
  TH.gene.exp.freq.train.pos = 0.8,
  TH.gene.exp.freq.train.neg = 0.2,
  TH.silhouette = -Inf,
  RF.selectVar = F,
  ...
)

Arguments

obj.list	object; named list of object of singleCellExperiment class
gene.core.tb	data.frame; signature genes
pca.rotation	matrix; rotation matrix (default: NULL)
assay.name	character; which assay (default: "exprs")
out.prefix	character; output prefix (default: NULL).
adjB	character; batch column of the colData(obj). (default: NULL)
meta.cluster	character; (default: NULL)
method	character; (default: "posFreq")
gene.pos.tb	data.frame; signature genes (positive)
gene.neg.tb	data.frame; signature genes (negative)
meta.info.tb	data.frame; cell information table (default: NULL)
meta.train.tb	data.frame; cell information table (default: NULL)
ndownsample	integer; number of cells (default: 1500)
myseed	integer; seed for random number generation.(default: 123456)
verbose	logical; (default: FALSE)
sig.prevelance	double; (default: 0.5)
ntop	integer; only use the ntop top genes (default: 10)
ncores	integer; number of CPU to used (default: 16)
bin.z.pos.th	numeric; z score of 'epressed' genes must be larger than this value (default: 0.3)
bin.z.neg.th	numeric; z score of 'not epressed' genes must be less than this value (default: 0.3)
prob.th	numeric; probability threshold (default: 0.8)
TH.gene.exp.freq	double; for a panel of signature genes, it will be classified as expressed if more than this value of genes are expressed (default: 0.65)
TH.gene.exp.freq.train.pos	double; for a panel of signature genes, it will be classified as positive instance if more than this value of genes are expressed (default: 0.8)
TH.gene.exp.freq.train.neg	double; for a panel of signature genes, it will be classified as negative instance if less than this value of genes are expressed (default: 0.2)
TH.silhouette	double; threshold (default: -Inf)
RF.selectVar	logical; (default: FALSE)
...	parameters passed to some method

Details

classify cells using the signature genes

Japrin/sscClust documentation built on Dec. 15, 2022, 1:04 p.m.