SiftCellBoost: This function runs SiftCell-Boost, it generates a file of...

In jyxi7676/SiftCell: SiftCell framework to identify cell containing and cell free droplets

This function runs SiftCell-Boost, it generates a file of barcode of infered cell-containing droplets

Description

This function runs SiftCell-Boost, it generates a file of barcode of infered cell-containing droplets

Usage

SiftCellBoost(
  workingdir,
  threshold = 100,
  expectedN = 1000,
  dataName = "Sample",
  mitoGenes = TRUE,
  otherFlagGenes = NULL,
  N.PCs = 100,
  geneUMIthreshold = 50,
  seed = 0,
  quantileReg = FALSE,
  labels = FALSE
)

Arguments

workingdir	working director with DGE and shuffleDGE two folders. Within DGE or shuffleDGE foler,
threshold	UMI threshold; By default threshold = 100
expectedN	number of expected cell-containing droplets in the dataset.
dataName	name of the dataset. For example:PBMC
mitoGenes	Default true
otherFlagGenes	f0lag genes that characterize unwanted celltypes. For example:PPBP, a marker
N.PCs	PCs
geneUMIthreshold	genes less than the threshold is discarded
seed	seed for randomization
quantileReg	default if use top 1000 HVG
labels	external labels

jyxi7676/SiftCell documentation built on July 27, 2023, 7:13 a.m.