parallel_sample_ichor_capture: IchorCNA implementation for Capture Panel Data

In TearsWillFall/ULPwgs: An implementation of a wrapper for estimating tumor fraction in ultra-low-pass whole genome sequencing (ULP-WGS) for cell-free DNA in GNU/Unix based systems

IchorCNA implementation for Capture Panel Data

Description

IchorCNA implementation for Capture Panel Data

Usage

parallel_sample_ichor_capture(
  cnrs = "",
  patient_id = "",
  normal = 0.5,
  ploidy = 2,
  maxCN = 7,
  includeHOMD = FALSE,
  scStates = c(1, 3),
  txnE = 0.9999999,
  txnStrength = 1e+07,
  output_dir = ".",
  min_cov = -15,
  lambda = NULL,
  coverage = NULL,
  minSegmentBins = 50,
  minTumFracToCorrect = 0.01,
  chrs = c(1:22, "X"),
  chrTrain = seq(1:22),
  gender = "male",
  maxFracCNASubclone = 0.7,
  maxFracGenomeSubclone = 0.5,
  lambdaScaleHyperParam = 3,
  altFracThreshold = 0.05,
  estimateNormal = TRUE,
  estimatePloidy = TRUE,
  estimateScPrevalence = TRUE,
  plotYLim = c(-2, 2),
  plotFileType = "pdf",
  verbose = FALSE,
  batch_config = build_default_preprocess_config(),
  threads = 4,
  ram = 4,
  mode = "local",
  executor_id = make_unique_id("parSamplehybridIchorCNA"),
  task_name = "parSamplehybridIchorCNA",
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

cnrs	REQUIRED Path to tumour CNR file.
normal	OPTIONAL Path to normal samples. Default c(0.5,0.6,0.7,0.8,0.9)
ploidy	OPTIONAL Initial tumour ploidy; can be more than one value if additional ploidy initializations are desired. Default: 2
maxCN	OPTIONAL Total clonal states. Default 7.
includeHOMD	OPTIONAL If FALSE, then exclude HOMD state. Useful when using large bins (e.g. 1Mb). Default FALSE.
scStates	OPTIONAL Subclonal states to consider. Default NULL
txnE	OPTIONAL Self-transition probability. Increase to decrease number of segments. Default: 0.9999999
txnStrength	OPTIONAL Transition pseudo-counts. Exponent should be the same as the number of decimal places of –txnE. Default: 1e+07
output_dir	OPTIONAL Path to the output directory.
lambda	OPTIONAL Initial Student's t precision; must contain 4 values (e.g. c(1500,1500,1500,1500)); if not provided then will automatically use based on variance of data
minSegmentBins	OPTIONAL Minimum number of bins for largest segment threshold required to estimate tumor fraction; if below this threshold, then will be assigned zero tumor fraction
maxFracCNASubclone	OPTIONAL Exclude solutions with fraction of subclonal events greater than this value. Default 0.7
maxFracGenomeSubclone	OPTIONAL Exclude solutions with subclonal genome fraction greater than this value. Default 0.5
lambdaScaleHyperParam	OPTIONAL Hyperparameter (scale) for Gamma prior on Student's-t precision. Default 3
altFracThreshold	OPTIONAL Minimum proportion of bins altered required to estimate tumor fraction; if below this threshold, then will be assigned zero tumor fraction. Default: 0.05
estimateNormal	OPTIONAL Estimate normal. Default TRUE.
estimatePloidy	OPTIONAL Estimate tumour ploidy. Default TRUE.
estimateScPrevalence	OPTIONAL Estimate subclonal prevalence. Default TRUE.
plotYLim	OPTIONAL ylim to use for chromosome plots. Default: c(-2,2)
plotFileType	OPTIONAL File format for output plots. Default pdf
verbose	OPTIONAL Enables progress messages. Default False.
threads	OPTIONAL Number of threads to split the work. Default 4
ram	OPTIONAL RAM memory to asing to each thread. Default 4
mode	REQUIRED Where to parallelize. Default local. Options "local","batch"
executor_id	Task EXECUTOR ID. Default "recalCovariates"
task_name	Task name. Default "recalCovariates"
time	OPTIONAL If batch mode. Max run time per job. Default "48:0:0"
update_time	OPTIONAL If batch mode. Job update time in seconds. Default 60.
wait	OPTIONAL If batch mode wait for batch to finish. Default FALSE
hold	OPTIONAL HOld job until job is finished. Job ID.
output_name	OPTIONAL Name for the output. If not given the name of the first tumour sample of the samples will be used.

TearsWillFall/ULPwgs documentation built on April 18, 2024, 3:45 p.m.