binning: Calculates genomic bins with GC content and mappability

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

Calculates genomic bins with GC content and mappability

Description

Calculates genomic bins with GC content and mappability

Usage

binning(
  RefGenome,
  bowtie2_index,
  bin_size = 20 * 10^3,
  read_size = 40,
  fragment_size = 200,
  paired_ends = F,
  directory_to_bamfiles = NULL,
  tmp_dir = file.path(getwd(), "bins"),
  upper_mappability_th = 1.5,
  lower_mappability_th = 0.8,
  black_list = NULL,
  coverage = 1,
  errorRate = 10^-3,
  chr_prefix = "chr",
  chr_range = NULL,
  cores = 1,
  return_estimated_param = F
)

Arguments

RefGenome,	path to .fa file
bowtie2_index,	bowtie2 index
bin_size,	size of the final bin in bp: default = 20 000
read_size,	size of a read in bp: default= 40bp
fragment_size,	size of a fragment in bp if paired_ends=T: default= 200bp
paired_ends,	logical, whether reads have to be PE or SE: default= False
directory_to_bamfiles,	path to bam file folder from which estimate read_size, fragment_size and paired_ends.
tmp_dir,	path where to create a temporary folder: default= bins in the wd
upper_mappability_th,	max mappability above which a bin is considered unsuitable for the analysis
lower_mappability_th,	min mappability below which a bin is considered unsuitable for the analysis
black_list,	path to a blacklist file
coverage,	an integer corresponding to the simulated coverage
errorRate,	simulated sequencer percentage error rate
chr_prefix,	prefix identifying a chromosome in the .fa file: default='chr'
chr_range,	chromosomes to consider in the analysis. Use ':' to identify a range and ',' for isolated chromosomes. default='1:22'
cores,	number of cores to use
return_estimated_param,	logical value. If True and directory_to_bamfiles has been passed it returns a list wit the estimated parameters and the calculated bins

Value

dataframe

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