[R] help with nesting if else statements

[Jeremie Juste]

Hello Ana Marija,

I cannot reproduce your error,

with a$PHENO=ifelse(a$PLASER==2 |a$RTNPTHY==2, 2, ifelse(a$CURRELIG==1 | a$RTNPTHY==1,1,NA))
For instance I have the expected PHENO=2

>     FID      IID   CURRELIG  PLASER  RTNPTHY PHENO
> 39: fam5706 G5706        1      1       2     2

In general I find nested ifelse to be difficult to work with especially
when I am tired :-). I would suggest this alternative way instead. It uses
data.table and you can investigate each step if you need to.

library(data.table)
setDT(a)
a[,PHENO:=NA]
a[PLASER==2|RTNPTHY==2,PHENO:=2]
a[is.na(PHENO)&(CURRELIG==1|RTNPTHY==1),PHENO:=1]


HTH,
Jeremie

a <- read.table(text="FID,IID,CURRELIG,PLASER,RTNPTHY
fam5610,G5610,1,1,1
fam5614,G5614,1,2,2
fam5615,G5615,1,1,1
fam5618,G5618,1,1,2
fam5621,G5621,1,1,1
fam5624,G5624,1,1,2
fam5625,G5625,1,1,1
fam5628,G5628,1,2,2
fam5633,G5633,1,2,2
fam5634,G5634,1,1,1
fam5635,G5635,2,2,2
fam5636,G5636,1,1,1
fam5641,G5641,1,1,1
fam5645,G5645,2,1,2
fam5646,G5646,2,2,2
fam5654,G5654,1,2,2
fam5655,G5655,1,2,2
fam5656,G5656,2,2,2
fam5658,G5658,1,1,1
fam5659,G5659,2,2,2
fam5660,G5660,1,1,1
fam5661,G5661,2,2,2
fam5664,G5664,1,1,1
fam5666,G5666,1,1,1
fam5667,G5667,1,1,2
fam5670,G5670,1,1,1
fam5671,G5671,1,1,2
fam5672,G5672,1,1,2
fam5673,G5673,1,1,1
fam5680,G5680,1,2,2
fam5686,G5686,1,2,2
fam5687,G5687,1,2,2
fam5688,G5688,1,1,2
fam5693,G5693,2,1,1
fam5695,G5695,1,1,1
fam5697,G5697,1,1,1
fam5700,G5700,1,2,2
fam5701,G5701,1,1,1
fam5706,G5706,1,1,2
fam5709,G5709,1,1,1
fam5713,G5713,1,1,1
fam5715,G5715,1,1,1
fam5718,G5718,1,1,1",sep=",", header=TRUE)