prepareData: prepareData

In wguo-research/scCancer: A package for automated processing of single cell RNA-seq data in cancer

prepareData

Description

prepareData

Usage

prepareData(
  samplePath,
  species = "human",
  hg.mm.mix = F,
  hg.mm.thres = 0.9,
  mix.anno = c(human = "hg19", mouse = "mm10")
)

Arguments

samplePath	A path containing the cell ranger processed data.
species	A character string indicating what species the sample belong to. Must be one of "human"(default) and "mouse".
hg.mm.mix	A logical value indicating whether the sample is a mix of human cells and mouse cells(such as PDX sample). If TRUE, the arguments 'hg.mm.thres' and 'mix.anno' should be set to corresponding values.
hg.mm.thres	A float-point threshold within [0.5, 1] to identify human and mouse cells. Cells with UMI percentage of single species larger than the threshold are labeled human or mouse cells. The default is 0.6.
mix.anno	A vector to indicate the prefix of genes from different species. The default is c("human" = "hg19", "mouse" = "mm10").

Value

A list of expr.data, cell.manifest, gene.manifest, raw.data, min.nUMI, cr.version and run.emptydrop

wguo-research/scCancer documentation built on May 26, 2024, 9:12 p.m.