cnvInfer: Inferring CNV using different methods

In WubingZhang/scAnalyzer: Integrative analysis pipeline for analyzing single-cell RNA-seq data

Inferring CNV using different methods

Description

Inferring CNV using different methods

Usage

cnvInfer(
  SeuratObj,
  group.by = "seurat_clusters",
  normal_groups = NULL,
  methods = c("infercnv"),
  nthreads = 8,
  outdir = "./",
  gene_order_file = NULL
)

Arguments

SeuratObj	A seurat object including count matrix and cell cluster annotation.
group.by	An integer or a character specifying the cell cluster column in the seurat meta.data.
normal_groups	A vector specifying the groups of normal cells, which mush match the name shown in meta.data.
methods	copykat, infercnv, numbat
nthreads	An integer specifying the number of threads for running inferCNV
outdir	path to output intermediate results.
gene_order_file	path to the gene order file (required for infercnv); using geneorder_hg20 by default.

Value

A seurat object with prediction results added into meta.data.

Author(s)

Wubing Zhang

WubingZhang/scAnalyzer documentation built on Jan. 30, 2023, 10:11 p.m.