Package 'DoAbsolute' reference manual

Title:	Automate Absolute Copy Number Calling
Description:	Provide an easy interface to automate estimation of absolute copy number, purity, ploidy using 'ABSOLUTE'.
Authors:	Shixiang Wang [aut, cre]
Maintainer:	Shixiang Wang <[email protected]>
License:	MIT + file LICENSE
Version:	2.2.0
Built:	2024-11-19 04:39:48 UTC
Source:	https://github.com/ShixiangWang/DoAbsolute

Automate ABSOLUTE calling for multiple samples in parallel way

Description

An example can be found at README. If calling for a sample failed, the error message will be written to error.log under result directory.

Usage

DoAbsolute(
  Seg,
  Maf = NULL,
  sigma.p = 0,
  max.sigma.h = 0.2,
  min.ploidy = 0.5,
  max.ploidy = 10,
  primary.disease = NA,
  platform = c("SNP_6.0", "Illumina_WES", "SNP_250K_STY"),
  temp.dir = file.path(tempdir(), "Absolute"),
  clean.temp = FALSE,
  results.dir = getwd(),
  max.as.seg.count = 1500,
  max.non.clonal = 0.05,
  max.neg.genome = 0.005,
  copy.num.type = c("total", "allelic"),
  min.mut.af = 0.1,
  min.no.mut = 5,
  verbose = FALSE,
  nThread = 1L,
  keepAllResult = TRUE,
  recover = FALSE
)
DoAbsolute(
  Seg,
  Maf = NULL,
  sigma.p = 0,
  max.sigma.h = 0.2,
  min.ploidy = 0.5,
  max.ploidy = 10,
  primary.disease = NA,
  platform = c("SNP_6.0", "Illumina_WES", "SNP_250K_STY"),
  temp.dir = file.path(tempdir(), "Absolute"),
  clean.temp = FALSE,
  results.dir = getwd(),
  max.as.seg.count = 1500,
  max.non.clonal = 0.05,
  max.neg.genome = 0.005,
  copy.num.type = c("total", "allelic"),
  min.mut.af = 0.1,
  min.no.mut = 5,
  verbose = FALSE,
  nThread = 1L,
  keepAllResult = TRUE,
  recover = FALSE
)

Arguments

`Seg`	a `data.frame` or a file (path) contains columns "Sample", "Chromosome", "Start", "End", "Num_Probes", "Segment_Mean".
`Maf`	MAF, default is `NULL`, can provided as `data.frame` or file path.
`sigma.p`	Provisional value of excess sample level variance used for mode search. Default: 0
`max.sigma.h`	Maximum value of excess sample level variance (Eq. 6). Default: 0.2
`min.ploidy`	Minimum ploidy value to consider. Solutions implying lower ploidy values will be discarded. Default: 0.5
`max.ploidy`	Maximum ploidy value to consider. Solutions implying greater ploidy values will be discarded. Default: 10
`primary.disease`	Primary disease of the sample. Default: `NA`
`platform`	one of "SNP_6.0", "Illumina_WES", "SNP_250K_STY". Default: "SNP_6.0"
`temp.dir`	directory path used to store tempory files. Default: Absolute subdirectory under `tempdir()`
`clean.temp`	if `TRUE`, auto-clean temp dir at the end. Default: `FALSE`
`results.dir`	directory path used to store result files. Default: work directory
`max.as.seg.count`	Maximum number of allelic segments. Samples with a higher segment count will be flagged as 'failed'. Default: 1500
`max.non.clonal`	Maximum genome fraction that may be modeled as non-clonal (subclonal SCNA). Solutions implying greater values will be discarded. Default: 0.05
`max.neg.genome`	Maximum genome fraction that may be modeled as non-clonal with copy-ratio below that of clonal homozygous deletion. Solutions implying greater values will be discarded. Default: 0.005
`copy.num.type`	The type of copy number to be handled. Either total or allelic. Total is what this package for. Default: "total"
`min.mut.af`	Minimum mutation allelic fraction. Mutations with lower allelic fractions will be filtered out before analysis. Default: 0.1
`min.no.mut`	Minor allele frequency file, or NULL if one is not available. This specifies the data for somatic point mutations to be used by ABSOLUTE. Default: 5
`verbose`	if `TRUE`, print extra info. Default: `FALSE`
`nThread`	number of cores used for computation. Default: 1L
`keepAllResult`	if `TRUE`, clean all results, otherwise clean result directory and keep most important results. Default: `TRUE`
`recover`	if `TRUE`, recover previous unfinished work. This is helpful when program stop unexpectedly when `clean.temp` is FALSE. Default: `FALSE`

Details

ABSOLUTE is a famous software developed by Broad Institute, however the RunAbsolute function is designed for computing one sample each time and set no default values. DoAbsolute help user set default parameters according to ABSOLUTE documentation, provide an uniform interface to input data easily and run RunAbsolute parallelly.

More detail about how to analyze ABSOLUTE results please see this link.

Author(s)

Shixiang Wang [email protected]

References

Carter, Scott L., et al. "Absolute quantification of somatic DNA alterations in human cancer." Nature biotechnology 30.5 (2012): 413.

Package 'DoAbsolute'