data-raw/test-code/test-signature-attribution-SBS96.R

In steverozen/mSigAct.server: Shiny Server for Analyzing Mutational Signature Activities

catSBS96.1 <- PCAWG7::spectra$PCAWG$SBS96[, 1, drop = FALSE]
my.sig.SBS96 <- 
  mSigAct.server::CancerTypeToSigSubset(cancer.type = "Biliary-AdenoCA", tumor.cohort = "PCAWG",
                        sig.type = "SBS96", region = "genome")
library(mSigAct)
packageVersion("mSigAct")

mm <- DefaultManyOpts()
mm$trace <- 100


start.time.SBS96 <- Sys.time()
foo <- SparseAssignActivity(spectra = catSBS96.1, sigs = my.sig.SBS96,
                            max.level = 9, 
                            p.thresh = 0.01, 
                            m.opts = mm)
end.time.SBS96 <- Sys.time()
time.taken.SBS96 <- end.time.SBS96 - start.time.SBS96
time.taken.SBS96

start.time.SBS96.1 <- Sys.time()
foo <- SparseAssignActivity(spectra = catSBS96.1, sigs = my.sig.SBS96,
                            max.level = 17, 
                            p.thresh = 0.01, 
                            m.opts = mm,
                            mc.cores.per.sample = 100)
end.time.SBS96.1 <- Sys.time()
time.taken.SBS96.1 <- end.time.SBS96 - start.time.SBS96
time.taken.SBS96.1

my.sig.SBS96.2 <- my.sig.SBS96[, 1:17, drop = FALSE]
foo2 <- SparseAssignActivity(spectra = catSBS96.1, sigs = my.sig.SBS96.2,
                            max.level = 9, 
                            p.thresh = 0.01, 
                            m.opts = DefaultManyOpts()) 


my.sig.SBS96.3 <- my.sig.SBS96[, 1:16, drop = FALSE]
foo3 <- SparseAssignActivity(spectra = catSBS96.1, sigs = my.sig.SBS96.3,
                             max.level = 17, 
                             p.thresh = 0.01, 
                             m.opts = DefaultManyOpts()) 

my.sig.SBS96.4 <- my.sig.SBS96[, 1:15, drop = FALSE]
foo4 <- SparseAssignActivity(spectra = catSBS96.1, sigs = my.sig.SBS96.4,
                             max.level = 15, 
                             p.thresh = 0.01, 
                             m.opts = DefaultManyOpts()) 

my.sig.SBS96.5 <- my.sig.SBS96[, 1:14, drop = FALSE]
foo4 <- SparseAssignActivity(spectra = catSBS96.1, sigs = my.sig.SBS96.5,
                             max.level = 14, 
                             p.thresh = 0.01, 
                             m.opts = DefaultManyOpts())