DoAbsolute: Automate ABSOLUTE calling for multiple samples in parallel...

View source: R/DoAbsolute.R

DoAbsoluteR Documentation

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
)

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 w_shixiang@163.com

References

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


ShixiangWang/DoAbsolute documentation built on Jan. 4, 2024, 5:16 a.m.