runScStatistics: runScStatistics

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

runScStatistics

Description

perform cell QC, gene QC, visualization and give suggested thresholds.

Usage

runScStatistics(
  dataPath,
  savePath,
  authorName = NULL,
  sampleName = "sc",
  species = "human",
  hg.mm.mix = F,
  hg.mm.thres = 0.6,
  mix.anno = c(human = "hg19", mouse = "mm10"),
  bg.spec.genes = NULL,
  bool.runSoupx = F,
  genReport = T
)

Arguments

dataPath	A path containing the cell ranger processed data. Under this path, folders 'filtered_feature_bc_matrix' and 'raw_feature_bc_matrix' exist generally.
savePath	A path to save the results files(suggest to create a foler named by sample name).
authorName	A character string for authors name and will be shown in the report.
sampleName	A character string giving a label for this sample.
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").
bg.spec.genes	A list of backgroud specific genes, which are used to remove ambient genes' influence.
bool.runSoupx	A logical value indicating whether to estimate contamination fraction by SoupX.
genReport	A logical value indicating whether to generate a .html/.md report (suggest to set TRUE).

Value

A results list with all useful objects used in the function.

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