Question: survival analysis in R
0
gravatar for jyotsnap
7 weeks ago by
jyotsnap0
jyotsnap0 wrote:

how to derive overall survival from geo dataset in R studio, please mention code and packages to install also

R • 193 views
ADD COMMENTlink modified 5 weeks ago • written 7 weeks ago by jyotsnap0

Thankyou for providing link...will you please help me in coding of dataset GSE 29272(Gastric cancer) ...i have to get overall analysis report of this particular dataset survival analysis in R

ADD REPLYlink written 7 weeks ago by jyotsnap0
library(survival)
  library(RegParallel)

  res <- RegParallel(
    data = coxdata,
    formula = 'Surv(Time.RFS, Distant.RFS) ~ [*]',
    FUN = function(formula, data)
      coxph(formula = formula,
        data = data,
        ties = 'breslow',
        singular.ok = TRUE),
    FUNtype = 'coxph',
    variables = colnames(coxdata)[9:ncol(coxdata)],
    blocksize = 2000,
    cores = 2,
    nestedParallel = FALSE,
    conflevel = 95)
  res <- res[!is.na(res$P),]
  res

please explain this part of code (survival analysis in R) for getting hazard ratio...what is formula, data and breslow, please clarify

ADD REPLYlink modified 5 weeks ago by genomax89k • written 5 weeks ago by jyotsnap0

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized. SUBMIT ANSWER is for new answers to original question.

ADD REPLYlink written 5 weeks ago by genomax89k
3
gravatar for Kevin Blighe
7 weeks ago by
Kevin Blighe65k
Kevin Blighe65k wrote:

Sure, you want a beer with that, too?

Take a look: Survival analysis with gene expression

Kevin

ADD COMMENTlink written 7 weeks ago by Kevin Blighe65k

l

ibrary(survival) library(RegParallel)

res <- RegParallel( data = coxdata, formula = 'Surv(Time.RFS, Distant.RFS) ~ [*]', FUN = function(formula, data) coxph(formula = formula, data = data, ties = 'breslow', singular.ok = TRUE), FUNtype = 'coxph', variables = colnames(coxdata)[9:ncol(coxdata)], blocksize = 2000, cores = 2, nestedParallel = FALSE, conflevel = 95) res <- res[!is.na(res$P),] res

please explain this part of code (survival analysis in R) for getting hazard ratio...what is formula, data and breslow, please clarify

ADD REPLYlink modified 5 weeks ago by Kevin Blighe65k • written 5 weeks ago by jyotsnap0

please research these things yourself.

ADD REPLYlink written 5 weeks ago by Kevin Blighe65k
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