survival fit for TCGAmutsurv
survfitByGene(x, genesym)instance of TCGAmutsurv
character(1) presence or absence of mutation in this gene is used as stratifier
sk = build_surv_for_mut("SKCM")
#> snapshotDate(): 2023-04-24
#> Working on: SKCM_Mutation-20160128
#> see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
#> loading from cache
#> Working on: SKCM_colData-20160128
#> see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
#> loading from cache
#> Working on: SKCM_metadata-20160128
#> see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
#> loading from cache
#> Working on: SKCM_sampleMap-20160128
#> see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
#> loading from cache
#> harmonizing input:
#> removing 5442 sampleMap rows not in names(experiments)
#> removing 127 colData rownames not in sampleMap 'primary'
#> Error in TCGAprimaryTumors(proj): could not find function "TCGAprimaryTumors"
sk = survfitByGene(sk, "BRAF")
#> Error in eval(expr, envir, enclos): object 'sk' not found
plot( sk$survfit, lty=1:2, lwd=2, col=c("blue", "orange"))
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'plot': object 'sk' not found
title("BRAF mutation in SKCM")
#> Error in title("BRAF mutation in SKCM"): plot.new has not been called yet