compare multiple tumor times with respect to survival
compare_tumors(types = c("BRCA", "GBM"), ...)character() TCGA project codes
passed to `build_surv_for_mut`
a list of lists of two elements: survlist (Surv objects) and mutlist (mutation matrices)
cmp = compare_tumors()
#> snapshotDate(): 2023-04-24
#> 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'
#> Error in TCGAprimaryTumors(proj): could not find function "TCGAprimaryTumors"
plot(survfit(cmp$survlist[[1]]~1), conf.int=FALSE, xlab="years", ylab="Survival prob.", main="TCGA survival", lwd=2)
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'plot': object 'cmp' not found
lines(survfit(cmp$survlist[[2]]~1), lwd=2, lty=2, conf.int=FALSE)
#> Error in eval(predvars, data, env): object 'cmp' not found
legend(15, .98, lty=c(1,2), lwd=2, legend=c("BRCA", "GBM"), bty="n")
#> Error in (function (s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...) { if (!is.null(vfont)) vfont <- c(typeface = pmatch(vfont[1L], Hershey$typeface), fontindex = pmatch(vfont[2L], Hershey$fontindex)) .External.graphics(C_strWidth, as.graphicsAnnot(s), pmatch(units, c("user", "figure", "inches")), cex, font, vfont, ...)})(dots[[1L]][[1L]], cex = dots[[2L]][[1L]], font = dots[[3L]][[1L]], units = "user"): plot.new has not been called yet