README.md
In Sun-lab/SMASH: Subclone Multiplicity Allocation and Somatic Heterogeneity

CRAN status

What is this for?
Installation
Vignette
Workflow
Citation
Contact
FAQs

This package is designed to cluster somatic mutations called from a tumor sample with a matched normal sample. Each mutation is assumed to lie in a genomic segment of clonal copy number. Each mutation's inferred clonal copy number and the tumor purity estimate is required as input to successfully run the program. This information can be obtained by running algorithms such as ABSOLUTE or ASCAT that derive tumor purity and clonal copy number estimates from SNP Array intensities.

Visualizing subclone configurations.

Click to expand!

Copy/paste the following code into R/RStudio for SMASH installation.

pandoc = Sys.getenv("RSTUDIO_PANDOC")

cran_packs = c("Rcpp","RcppArmadillo","devtools","smarter","SMASH")
req_packs = c(cran_packs)

for(pack in req_packs){

    chk_pack = tryCatch(find.package(pack),
        error = function(ee){NULL})

    if( !is.null(chk_pack) ){
        library(pack,character.only = TRUE)
        next
    }

    if( pack %in% cran_packs ){
        install.packages(pack,dependencies = TRUE)
    }

}

To see the vignette, follow the code below. The vignette contains background knowledge and code to perform simulation, optimization, interpretation, and visualization.

library(SMASH)
vignette(package = "SMASH",topic = "intro")

flowchart LR

%% Nodes and directions
fasta{{reference.fasta}} & tbam{{tumor.bam}} & nbam{{normal.bam}} --> caller{{Variant Caller}}
caller --> vcf{{somatic.vcf}}
array{{SNP array data}} --> cnaCall{{Copy Number Algorithm}}
cnaCall --> cnaEst{{Purity, Allelic Copy Numbers}}
cnaEst & vcf --> SMASH{{SMASH}}

%% Class definitions
classDef myred fill:#f44336,stroke:#f3f6f4,stroke-width:2px
classDef myblue fill:#19daf8,stroke:#f3f6f4,stroke-width:2px
classDef mygreen fill:#79d50d,stroke:#f3f6f4,stroke-width:2px
classDef mymagenta fill:#fc9ffc,stroke:#f3f6f4,stroke-width:2px
classDef myyellow fill:#f6fa13,stroke:#f3f6f4,stroke-width:2px
classDef myorange fill:#f89d3e,stroke:#f3f6f4,stroke-width:2px

%% Assign classes to nodes
class tbam myred
class nbam myblue
class array myyellow
class fasta mygreen
class caller,cnaCall,SMASH myorange
class vcf,cnaEst mymagenta

Little, P., Lin, D.Y., Sun, W. (2019). Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time. Genome medicine, 11(1), 1-15. [HTML, PDF, Supplement]