classifyCell.by.sigGene: classify cells using signature genes
In Japrin/sscClust: simpler single cell RNAseq data clustering

classifyCell.by.sigGene

R Documentation

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