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survival analysis in R

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

r
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written by jyotsnap • jyotsnap

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

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written by jyotsnap • jyotsnap 
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

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updated by GenoMax GenoMax • written by jyotsnap • jyotsnap

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.

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written by GenoMax GenoMax

1 answer

Sure, you want a beer with that, too?

Take a look: Survival analysis with gene expression

Kevin

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written by Kevin Blighe Kevin Blighe

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

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updated by Kevin Blighe Kevin Blighe • written by jyotsnap • jyotsnap

please research these things yourself.

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written by Kevin Blighe Kevin Blighe

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