runCopyKAT: runCopyKAT

In Miaoyx323/stCancer: stCancer

runCopyKAT

Description

Analyze CNV using R package copyKAT Gao, R., Bai, S., Henderson, Y. C., Lin, Y., Schalck, A., Yan, Y., Kumar, T., Hu, M., Sei, E., Davis, A., Wang, F., Shaitelman, S. F., Wang, J. R., Chen, K., Moulder, S., Lai, S. Y. & Navin, N. E. (2021). Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes. Nat Biotechnol. doi:10.1038/s41587-020-00795-2.

Usage

runCopyKAT(
  SeuratObject,
  savePath,
  cluster.info = "seurat_clusters",
  id.type = "S",
  ngene.chr = 5,
  win.size = 25,
  KS.cut = 0.1,
  n.cores = 1,
  sam.name = "test",
  distance = "euclidean",
  norm.cell.names = "",
  output.seg = "FLASE",
  ...
)

Arguments

SeuratObject	A seuratObejct to analyze CNV
savePath	A path to store the results
cluster.info	The label to store cluster information in '[e-mail]'
id.type	The parameter of copyKAT
ngene.chr	The parameter of copyKAT
win.size	The parameter of copyKAT
KS.cut	The parameter of copyKAT
n.cores	The parameter of copyKAT
sam.name	The parameter of copyKAT
distance	The parameter of copyKAT
norm.cell.names	The parameter of copyKAT
output.set	The parameter of copyKAT

Value

A list containing a seuratObject, a list of results of intermediate process, a list of plots and a logical value to show whether the process completed successfully

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