compare multiple tumor times with respect to survival

compare multiple tumor times with respect to survival

compare_tumors(types = c("BRCA", "GBM"), ...)

Arguments

types

character() TCGA project codes

...

passed to `build_surv_for_mut`

Value

a list of lists of two elements: survlist (Surv objects) and mutlist (mutation matrices)

Examples

cmp = compare_tumors()
#> snapshotDate(): 2023-04-04
#> Working on: BRCA_Mutation-20160128
#> see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
#> loading from cache
#> Working on: BRCA_colData-20160128
#> see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
#> loading from cache
#> Working on: BRCA_metadata-20160128
#> see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
#> loading from cache
#> Working on: BRCA_sampleMap-20160128
#> see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
#> loading from cache
#> harmonizing input:
#>   removing 14592 sampleMap rows not in names(experiments)
#>   removing 121 colData rownames not in sampleMap 'primary'
#> snapshotDate(): 2023-04-04
#> Working on: GBM_Mutation-20160128
#> see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
#> loading from cache
#> Working on: GBM_colData-20160128
#> see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
#> loading from cache
#> Working on: GBM_metadata-20160128
#> see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
#> loading from cache
#> Working on: GBM_sampleMap-20160128
#> see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
#> loading from cache
#> harmonizing input:
#>   removing 7756 sampleMap rows not in names(experiments)
#>   removing 309 colData rownames not in sampleMap 'primary'
plot(survfit(cmp$survlist[[1]]~1), conf.int=FALSE, xlab="years", ylab="Survival prob.", main="TCGA survival", lwd=2)
lines(survfit(cmp$survlist[[2]]~1), lwd=2, lty=2, conf.int=FALSE)
legend(15, .98, lty=c(1,2), lwd=2, legend=c("BRCA", "GBM"), bty="n")