abs_prepare: Prepare parameters for absCopyNumber calling

In ShixiangWang/absCopyNumber: Tumor Purity, Ploidy and Absolute Copy Number Estimation

Description

This is the second step for absCopyNumber pipeline, user provide parameters for model construction.

Usage

abs_prepare(absCopyNumber, alpha.min = 0.2, alpha.max = 1,
  tau.min = 0.5, tau.max = 8, copyratio.min = 0.2,
  copyratio.max = 3, qmax = 10, lamda = 0.5,
  method = c("Grid Search", "Bayesian Optimization"),
  min.sol.freq = 0.05, snv.type = c("somatic", "germline"))

Arguments

absCopyNumber	a absCopyNumber object generated by abs_initialize function.
alpha.min	the minimum allowed value for tumor purity. Default is 0.20. If you do have the pathologist estimate, set it as the lower bound of the pathologist estimate is usually preferred.
alpha.max	the maximum allowed value for tumor purity. Default is 1.0. If you do have the pathologist estimate, set it as the upper bound of the pathologist estimate is usually preferred.
tau.min	the minimum allowed value for tumor ploidy, default is 0.5.
tau.max	the maximum allowed value for tumor ploidy, default is 8.
copyratio.min	the minimum value of copy number ratio to assign weight in model, default is 0.2.
copyratio.max	the maximum value of copy number ratio to assign weight in model, default is 3.
qmax	maximum allowed absolute copy number for any segments, default is 10.
lamda	The relative weight of the segment copy ratio data over the SNV data. Must be a value in (0.0,1.0]. Only used when SNV file is provided. The default value is 0.5, which give equal weights to copy-number-based ratio estimator and SNV-frequency-based estimator. If lamda is 1, only use copy-number-based ratio model to minimized objective function.
method	method for object function optimization, should be one of "Grid Search", "Bayesian Optimization".
min.sol.freq	A solution should appear at least this proportion to be kept. Singleton solutions are usually not trustable. By default (min.sol.freq=0.05), the program will only retain solutions that cover at least 5 percent of the search space.
snv.type	one of "somatic", "germline", if no SNV data, just let is be "somatic"

Value

a absCopyNumber object with parameters for model construction.

Author(s)

Shixiang Wang <[e-mail]>

See Also

absCopyNumber, abs_initialize, , abs_calling

Examples

file_cn = system.file("extdata/example.cn.txt.gz", package = "absCopyNumber")
file_snv = system.file("extdata/example.snv.txt.gz", package = "absCopyNumber")


res1 =  abs_initialize(seg = file_cn, snv = file_snv, verbose = T)
res1 =  abs_prepare(res1)

ShixiangWang/absCopyNumber documentation built on May 28, 2019, 5:42 p.m.