run_fromLocal: Run absCopyNumber from Local Files

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

Description

This wrapper function accepts data files and user specified parameters and runs the absCNseq algorithm from paper "AbsCN-seq: a statistical method to estimate tumor purity, ploidy and absolute copy numbers from next-generation sequencing data."

Usage

run_fromLocal(seg.fn, snv.fn = NULL, res.dir = NULL, sample.name,
  platform = c("WES", "WGS", "MicroArray"), alpha.min = 0.2,
  alpha.max = 1, tau.min = 0.5, tau.max = 8, min.sol.freq = 0,
  min.seg.len = NULL, qmax = 7, lamda = 0.5, verbose = FALSE)

Arguments

seg.fn	The name of the file containing the segmentation data. An example file called "example.cn.txt.gz" can be found under the "inst/extdata" folder within the package.
snv.fn	The name of the file containing a set of somatic single nucleotide variants (SNVs). An example file called "example.snv.txt.gz" can be found under the "inst/extdata" folder within the package.
res.dir	The output directory
sample.name	Sample name, used when store result to local machine.
platform	"WES" for whole exome sequencing, "WGS" for whole genome sequencing and "MicroArray" for SNP or other gene chips can detect CNV.
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.
min.sol.freq	A solution should appear at least this many times to be kept. Singleton solutions are usually not trustable. By default (min.sol.freq=0), the program will only retain solutions that cover at least 5 percent of the search space.
min.seg.len	The minimum length of a segment to be included in computation. The default value is 200 bp for WES, 3000 bp for WGS and 0 bp for MicroArray.
qmax	Maximum allowed absolute copy number for any segments, default is 7.
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.
verbose	if True, print extra output

Value

searchRes	a data frame giving the solution set (purity and ploidy pairs) ranked by their fitting errors
absCN	a data frame giving the absolute copy number estimates of tumor cells for the top first solution (purity and ploidy pair)
absSNV	a data frame giving the absolute multiplicity estimates of SNVs for the top first solution (purity and ploidy pair)
orig.seg.dat	original copy ratio data read from the input segmentation file
seg.dat	filtered copy ratio data
orig.snv.dat	original SNV data read from the input SNV file
snv.dat	filtered SNV data

Author(s)

Lei Bao, Shixiang Wang

References

AbsCN-seq: a statistical method to estimate tumor purity, ploidy and absolute copy numbers from next-generation sequencing data.

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