runMalignancy: runMalignancy

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

runMalignancy

Description

runMalignancy

Usage

runMalignancy(
  expr,
  gene.manifest,
  cell.annotation,
  savePath,
  cutoff = 0.1,
  minCell = 3,
  p.value.cutoff = 0.5,
  coor.names = c("tSNE_1", "tSNE_2"),
  ref.data = NULL,
  referAdjMat = NULL,
  species = "human",
  genome = "hg19",
  hg.mm.mix = F
)

Arguments

expr	A Seurat object.
gene.manifest	A data.frame of genes' manifest.
cell.annotation	A data.frame of cells' annotation.
savePath	A path to save the results files. If NULL, the 'statPath' will be used instead.
cutoff	The cut-off for min average read counts per gene among reference cells. The default is 0.1.
minCell	An integer number used to filter gene. The default is 3.
p.value.cutoff	The p-value to decide whether the distribution of malignancy score is bimodality.
coor.names	A vector indicating the names of two-dimension coordinate used in visualization.
ref.data	An expression matrix of gene by cell, which is used as the normal reference. The default is NULL, and an immune cells or bone marrow cells expression matrix will be used for human or mouse species, respectively.
referAdjMat	An adjacent matrix for the normal reference data. The larger the value, the closer the cell pair is. The default is NULL, and a SNN matrix of the default ref.data will be used.
species	A character string indicating what species the sample belong to. Only "human"(default) or "mouse" are allowed.
genome	A character string indicating the version of the reference gene annotation information. This information is mainly used to infer CNV profile and estimate malignancy. Only 'hg19' (defalut) or 'hg38' are allowed for "human" species, and only "mm10" is allowed for "mouse" species.
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.

Value

A list of cnvList, reference malignancy score, seurat object, cell.annotatino, bimodal.pvalue, malign.thres, and all generated plots.

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