runMalignancy: runMalignancy

In Miaoyx323/stCancer: stCancer

runMalignancy

Description

runMalignancy

Usage

runMalignancy(
  SeuratObject,
  savePath,
  assay = "Spatial",
  cutoff = 0.1,
  minspot = 3,
  p.value.cutoff = 0.5,
  coor.names = c("tSNE_1", "tSNE_2"),
  ref.object = NULL,
  species = "human",
  genome = "hg19"
)

Arguments

cutoff	The cut-off for min average read counts per gene among reference spots. The default is 0.1.
minspot	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.
expr	A Seurat object.
gene.manifest	A data.frame of genes' manifest.
spot.annotation	A data.frame of spots' annotation.
ref.data	An expression matrix of gene by spot, which is used as the normal reference. The default is NULL, and an immune spots or bone marrow spots 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 spot pair is. The default is NULL, and a SNN matrix of the default ref.data will be used.

Value

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

Miaoyx323/stCancer documentation built on Nov. 14, 2024, 5:31 p.m.