generate_CLONET_config: This function generates a config files for CLONET pipeline

In TearsWillFall/variantCall: An implementation of a wrapper for variant calling using MuTECT2 and Platypus GNU/Unix based systems

Description

This function takes multiple parameters and generates a config file for the CLONET tool

Usage

generate_CLONET_config(
  patient_id = "PATIENT",
  clonet_dir = "tools/CLONET",
  snp_dir = "",
  segment_data = "",
  sample_info = "",
  min_snp_cov = 10,
  min_nsnps = 10,
  min_seg_cov = 20,
  equal_betaThr = 0.9,
  max_homo_dels = 0.01,
  del_log_thr = c(-1, -0.25),
  alpha_par = 0.9,
  clonal_thr = 0.85,
  beta_thr = 0.85,
  stages = c(1, 2, 3, 4, 5, 6),
  comp_ref_map_bias = FALSE,
  beta_decimals = 3,
  ale_imb_thr = 0.5,
  beta_method = "STM",
  adm_method = "2D",
  jobs = 1,
  threads = 3,
  output_dir = ""
)

Arguments

patient_id	Patient ID. Default Patient
clonet_dir	Path to CLONET dir
snp_dir	Path to formated SNP data dir.
segment_data	Path to file with formated segment data.
sample_info	Path to file with sample info data.
min_snp_cov	Minimum tumor coverage for informative SNPs. Default 10.
min_nsnps	Minimum number of SNPs per segment. Default 10.
min_seg_cov	Minimum segment coverage. Default 20.
equal_betaThr	Minimum value of beta above which the two alleles are present in the same number. Default 0.9
max_homo_dels	Homozygous deletions threshold. Default 0.01
del_log_thr	Parameters of a valid deletion used to compute Adm.global. Default c(-1,-0.25)
alpha_par	Percentage of used deletions to compute Adm.global varibility interval. Default 0.9
clonal_thr	Clonality value threshold. Default 0.85
beta_thr	Beta value threshold. Default 0.85
stages	Analysis stages to run trough.Default c(1,2,3,4,5,6)
comp_ref_map_bias	Compute reference mapping bias and to adjust beta estimation. Default FALSE
beta_decimals	Number of beta value decimals to report. Default 3
beta_method	Method for beta estimation. Default STM. Options STM/GB
adm_method	Method for admixture estimation. Default 2D. Options 1D/2D
jobs	Number of Samples to analyze in parallel. Default 1
threads	Number of threads per job to use. Default 3
output_dir	Path to the output directory.
verbose	Enables progress messages. Default FALSE.

TearsWillFall/variantCall documentation built on Oct. 15, 2021, 8:51 p.m.