CallCNV: Calls CNV over genomic bins defined by binning

In CL-CHEN-Lab/User_interface_for_Kronos_scRT: R-package and Shiny App interface for the analysis of single cell replication timing data

Calls CNV over genomic bins defined by binning

Description

Calls CNV over genomic bins defined by binning

Usage

CallCNV(
  directory,
  bins,
  chrom_size,
  basename = "Exp",
  group = NULL,
  tmp_dir = file.path(getwd(), "CNV"),
  min_n_reads = 2e+05,
  mim_mean_CN_accepted = 2,
  max_mean_CN_accepted = 8,
  ploidy = NULL,
  chr_prefix = "chr",
  chr_range = NULL,
  cores = 1
)

Arguments

directory,	Single cell Bamfiles directory
bins,	bins produced by binning
chrom_size,	a dataframe (chr=chrom name, size=chrom size)
basename,	sample name
group,	experimental group name
tmp_dir,	temporary folder.
min_n_reads,	Min n of reads to keep a cell in the analysis
mim_mean_CN_accepted,	Min mean CN accepted as result
max_mean_CN_accepted,	Max mean CN accepted as result
ploidy,	user estimated ploidy
chr_prefix,	Chromosome prefix, if there is no prefix use NULL
chr_range,	Chromosomes to consider in the analysis (example 1:5,8,15:18,X)
cores,	Number of cores to use

Value

list of dataframes

CL-CHEN-Lab/User_interface_for_Kronos_scRT documentation built on Aug. 1, 2022, 2:08 p.m.