runInferCNV: Run inferCNV

In ProfessionalFarmer/loonR: Common function in bioinformatics analysis

Run inferCNV

Description

Run inferCNV

Usage

runInferCNV(
  seurat.obj,
  ref_group_names = NULL,
  HMM = F,
  denoise = F,
  gene_pos = "~/ref/hg38/gencode.v44/human_genes_pos.txt",
  save_local_path = NULL,
  num_threads = 40,
  no_plot = FALSE
)

Arguments

ref_group_names	Reference cell type
HMM	when set to True, runs HMM to predict CNV level (default: FALSE)
denoise	If True, turns on denoising according to options below (default: FALSE)
gene_pos	gene order file
save_local_path	Path to save rds
num_threads	Default: 40
no_plot

ProfessionalFarmer/loonR documentation built on Oct. 9, 2024, 9:56 p.m.