RunCcubePipeline: Run Ccube analysis

In keyuan/ccube: ccube

Run Ccube analysis

Description

Run Ccube analysis

Usage

RunCcubePipeline(sampleName = NULL, dataFolder = NULL,
  resultFolder = NULL, makeFolders = F, runParser = F, variantCaller,
  cnaCaller = NULL, runAnalysis = F, runQC = F,
  runAnalysisSnap = F, runPcawgMergeQc = F, writeOutput = F,
  modelSV = F, allFormats = F, basicFormats = T, vcfFile = NULL,
  copyNumberFile = NULL, purity = NA, numOfClusterPool = NULL,
  numOfRepeat = NULL, epi = 0.001, tol = 1e-08, maxiter = 1000,
  multiCore = F, ccubeInputRDataFile = NULL,
  ccubeResultRDataFile = NULL, ssm = NULL, maxSnv = 1e+07,
  use = "use_base")

Arguments

sampleName	sample name
dataFolder	path to data folder that stores tmp result files
resultFolder	path to output formats files
makeFolders	flag to create data and results folders, default false
runParser	run parser
variantCaller	name of variant caller
cnaCaller	name of CNA caller
runAnalysis	run analysis
runQC	run QC
runAnalysisSnap	run a lite version of the main analysis
runPcawgMergeQc	run QC for PCAWG samples
writeOutput	write output into files
modelSV	using double break points model
allFormats	all PCAWG output formats
basicFormats	basic PCAWG output formats
vcfFile	path to vcf file
copyNumberFile	path to copy number file
purity	estimated purity of the sample
numOfClusterPool	candidates of number of clusters
numOfRepeat	number of repeat runs for each candidate number of clusters
epi	sequencing error
tol	convergence thershold
maxiter	maximum iteration
multiCore	use multiple cores for repeated runs
ccubeInputRDataFile	path to Ccube input Rdata
ccubeResultRDataFile	path to Ccube result Rdata
ssm	Ccube input data
maxSnv	maximum number of SNVs. Used in runParser mode
use	option for rough estimator for ccf

Value

returns a list including the prefered solution, res; annotated ssm, ssm; a list of all solutions, results; trace of ELBOs, lb; removed events, droppedSsm

keyuan/ccube documentation built on Jan. 11, 2023, 12:01 a.m.