yingya / doabsolute

:package: Automate Absolute Copy Number Calling using 'ABSOLUTE' package

DoAbsolute

"YingYa/DoAbsolute" forked from "ShixiangWang/DoAbsolute" on 20210929, then modified some code to reduce the memory usage when large samples running.

The goal of DoAbsolute is to automate ABSOLUTE calling for multiple samples in parallel way.

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 helps user set default parameters according to ABSOLUTE documentation, provides a uniform interface to input data easily and runs RunAbsolute parallelly.

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

Installation

You can install the released version of DoAbsolute with:

remotes::install_github("YingYa/DoAbsolute")

Install ABSOLUTE, the version provided by DoAbsolute is 1.0.6. You can find available versions at https://software.broadinstitute.org/cancer/cga/absolute_download. Users of DoAbsolute all should accept LICENCE from Firehose.

install.packages("numDeriv")
path_to_file = system.file("extdata", "ABSOLUTE_1.0.6.tar.gz", package = "DoAbsolute", mustWork = T)
install.packages(path_to_file, repos = NULL, type="source")

Example

This is a basic example which shows you how to run DoAbsolute using example data from ABSOLUTE documentation.

Load package.

library(DoAbsolute)

example_path = system.file("extdata", package = "DoAbsolute", mustWork = T)


library(data.table)
# Load Test Data ----------------------------------------------------------

# segmentation file
seg_normal =  file.path(example_path, "SNP6_blood_normal.seg.txt")
seg_solid  =  file.path(example_path, "SNP6_solid_tumor.seg.txt")
seg_metastatic  = file.path(example_path, "SNP6_metastatic_tumor.seg.txt")
# MAF file
maf_solid  = file.path(example_path, "solid_tumor.maf.txt")
maf_metastatic  = file.path(example_path, "metastatic_tumor.maf.txt")

# read data
seg_normal = fread(seg_normal)
seg_solid = fread(seg_solid)
seg_metastatic = fread(seg_metastatic)
maf_solid = fread(maf_solid)
maf_metastatic = fread(maf_metastatic)

# merge data
Seg = Reduce(rbind, list(seg_normal, seg_solid, seg_metastatic))
Maf = Reduce(rbind, list(maf_solid, maf_metastatic))

Seg$Sample = substr(Seg$Sample, 1, 15)
Maf$Tumor_Sample_Barcode = substr(Maf$Tumor_Sample_Barcode, 1, 15)

# test function
DoAbsolute(Seg = Seg, Maf = Maf, platform = "SNP_6.0", copy.num.type = "total",
           results.dir = "test", nThread = 2, keepAllResult = TRUE, verbose = TRUE)

Citation

Wang, Shixiang, et al. "The predictive power of tumor mutational burden 
    in lung cancer immunotherapy response is influenced by patients' sex." 
    International journal of cancer (2019).

Reference:

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