classifyCell.by.model: classify cells using pre-trained model

In Japrin/sscClust: simpler single cell RNAseq data clustering

classify cells using pre-trained model

Description

classify cells using pre-trained model

Usage

classifyCell.by.model(
  obj.list,
  mod.rf,
  assay.name = "exprs",
  out.prefix = NULL,
  adjB = NULL,
  meta.info.tb = NULL,
  pca.rotation = NULL,
  pad.missing = F,
  allZeroAsLow = F,
  verbose = F,
  ncores = 16,
  ...
)

Arguments

obj.list	object; named list of object of singleCellExperiment class
mod.rf	object; pre-trained model used for prediction
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.info.tb	data.frame; cell information table (default: NULL)
pca.rotation	matrix; rotation matrix (default: NULL)
pad.missing	logical; (default: FALSE)
allZeroAsLow	logical; (default: FALSE)
verbose	logical; (default: FALSE)
ncores	integer; number of CPU to used (default: 16)
...	parameters passed to some method

Details

classify cells using pre-trained model, which can be obtained by run classifyCell.by.sigGene()

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