scCNVPip: Run a post-quantification 10X technology-format single-cell...

In eudoraleer/Ursa: An Automated Multi-omics Package for Single-cell Analysis

Run a post-quantification 10X technology-format single-cell CNV (scCNV) pipeline

Description

This function will run a bioinformatics analysis of post-quantification scCNV pipeline. Supports multiple samples analysis.

Usage

scCNVPip(
  project_name = "Ursa_scCNV",
  input_dir = "./",
  output_dir = "./",
  pheno_file,
  confidence_threshold = 50,
  size_threshold = 2e+06,
  cnv_cell_threshold = 5
)

Arguments

project_name	Project name. 'Ursa_scCNV' by default.
input_dir	Directory to all input files. Current working directory by default.
output_dir	Output directory. Current working directory by default. A new folder with the given project name with time stamp as suffix will be created under the specified output directory.
pheno_file	Meta data file directory. Accept only .csv/.txt format files.
confidence_threshold	CNV event confidence threshold. Default is 50.
size_threshold	CNV event length. Default to 2Mbp in size.
cnv_cell_threshold	Filtering out CNV events that are present in less than N Values range from 0 to 100. Default to 5.

eudoraleer/Ursa documentation built on Nov. 26, 2022, 10:35 p.m.