Setting reference group for Hazard Ratio computed using coxph function in R

Question

when i run coxph(Surv(Time, Status)~Class, data = df) on data set like below it always sets the reference group by alphabetical order, in this case MutantA would be the reference group. Is there a way to tell it to make WT the reference group ?

df

Time    Status  Class
3   1   WT
4   1   WT
5   1   WT
7   1   WT
7   1   WT
7   1   WT
7   1   WT
2   1   WT
2   1   WT
2   1   WT
5   1   WT
6   1   WT
7   1   WT
8   1   MutantA
9   1   MutantA
2   1   MutantA
12  1   MutantA
3   1   MutantA
4   1   MutantA
5   1   MutantA
7   1   MutantA
7   1   MutantA
7   1   MutantA
7   0   MutantA
2   1   MutantA
2   1   MutantA
2   1   MutantA
5   1   MutantB
6   0   MutantB
7   1   MutantB
8   1   MutantB
9   1   MutantB
2   1   MutantB
12  1   MutantB
3   1   MutantB
4   0   MutantB
5   1   MutantB
7   1   MutantB
7   0   MutantB
7   1   MutantB
7   0   MutantB
2   1   MutantB
2   1   MutantB
2   1   MutantB
5   1   MutantB
6   1   MutantC
7   1   MutantC
8   1   MutantC
9   1   MutantC
2   1   MutantC
12  1   MutantC
11  1   MutantC
4   1   MutantC
3   1   MutantC
6   1   MutantC
7   1   MutantC
11  1   MutantC
3   1   MutantC
2   1   MutantC
6   1   MutantC

Answer 1

Yes, you just need you change the order the levels in your factor column  Class by making WT your first level:

df$Class <- factor(df$Class, levels = c("WT","MutantA","MutantB","MutantC"))
# or using Gregor's comment:
df$Class = relevel(df$Class, ref = "WT")
coxph(Surv(Time, Status)~Class, data  = df)

Call:
coxph(formula = Surv(Time, Status) ~ Class, data = df)

               coef exp(coef) se(coef)     z     p
ClassMutantA -0.557     0.573    0.406 -1.37 0.171
ClassMutantB -0.688     0.503    0.395 -1.74 0.082
ClassMutantC -0.689     0.502    0.401 -1.72 0.085