CODEWITHSUNDEEP
rformula
user2300940
user2300940

Reputation: 2385

Assign variable to coxph function

df.t <- structure(list(hsa_miR_105_5p = c(3.58497328179801, 5.73145238130165, 
1.19037294682376, -1.28586123284671, 1.27004401721869, 0.958088884635556
), hsa_miR_17_3p = c(1.21345556145455, 4.71642723353062, 5.87616915208789, 
0.776249937585565, 4.86437477300888, 1.71876771352689), hsa_miR_3916 = c(6.74863569372315, 
3.23155618956527, -0.105259761381448, -1.28586123284671, 4.60953338597123, 
2.95060221832751), hsa_miR_1295a = c(-1.35668910756094, 0.147551018264645, 
2.44220202218853, -1.28586123284671, 5.47367734142336, -0.135507425889107
)), row.names = c("86", "175", "217", "394", "444", "618"), class = "data.frame")

Time <- structure(c(1796, 1644.04166666667, 606.041666666667, 1327.04166666667, 
665, 2461), class = "difftime", units = "days")

Status <- c(0L, 0L, 1L, 0L, 1L, 0L)

FML <- as.formula(paste0('~',paste(colnames(df.t),collapse = '+')))

Using this input I would like use the FML object as input in the cox-model, however, this does not work. How can I define the FML object to be recognised by coxph?

coxph(Surv(Time, Status) FML, data = df.t)

Upvotes: 0

Views: 229

Answers (1)

MrFlick
MrFlick

Reputation: 206382

To combine the two formulas, you can use update.formula. For example

update.formula(Surv(Time, Status)~., FML)
# Surv(Time, Status) ~ hsa_miR_105_5p + hsa_miR_17_3p + hsa_miR_3916 + 
#    hsa_miR_1295a

So you can use that in your function

coxph(update.formula(Surv(Time, Status)~., FML), data = df.t)

That will return the same result as

coxph(Surv(Time, Status) ~ hsa_miR_105_5p + hsa_miR_17_3p + hsa_miR_3916 + 
  hsa_miR_1295a, data = df.t)

Upvotes: 1

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