On April 8, 2020 1:17:38 PM PDT, Ana Marija wrote:
| Hi,
| 
| I have a data frame like this:

Or ... *drum-roll* ... you could use plain 
old indexing.  Have a look:

a <-
"FID    LASER2  CURRELIG        PLASER  RTNPTHY
fam1000_G1000   1       1       1       1
fam1001_G1001   1       1       1       1
fam1003_G1003   2       1       2       2
fam1005_G1005   1       1       1       2
fam1009_G1009   1       1       1       2
fam1052_G1052   1       1       1       2"
a <- read.delim(text=a)

a$PHENO <- -9
a[a$CURRELIG==1 & a$RTNPTHY==1,"PHENO"] <- 1
a[a$PLASER==2,"PHENO"] <- 2

Best,
Rasmus

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