Hello,

Inline.

Às 22:44 de 29/04/20, Ana Marija escreveu:
Hi Rui,

thanks for getting back to me
so I tried your method and I got:
sum(b$PHENO==2, na.rm=T)
[1] 828
sum(b$PHENO==1, na.rm=T)
[1] 859

Can you please tell me if
b$PHENO <- (b$FLASER == 2 | b$PLASER == 2) + 1L

just assigns PHENO=2 if b$FLASER == 2 | b$PLASER == 2 and everything else is 1?

Yes, that's it. If b$FLASER == 2 | b$PLASER == 2 returns TRUE then adding 1 will give

TRUE + 1 -> 1 + 1 -> 2

This is because logical values are internally coded as integers 0 and 1.
And if the condition returns FALSE it becomes

FALSE + 1 -> 0 + 1 -> 1

In both cases the result is what you want.



Please see how my data looks like:
sum(b$FLASER==2, na.rm=T)
[1] 92
sum(b$FLASER==1, na.rm=T)
[1] 1533
sum(b$PLASER==1, na.rm=T)
[1] 850
sum(b$PLASER==2, na.rm=T)
[1] 806
dim(b)
[1] 1698    5
unique(b$FLASER)
[1]  1  3  2 NA
unique(b$PLASER)
[1]  1  2  3 NA


What I write above is valid even if your data contains NA's, like it does. This is because

(TRUE | x) == (x | TRUE) == TRUE

even if x is NA.

This is an example with some NA values in the data.

set.seed(1234)
b <- rbind(b, b)
i <- sample(nrow(b), 3)
b$FLASER[i] <- NA
i <- sample(nrow(b), 2)
b$PLASER[i] <- NA
b$PLASER[10] <- 2

b$PHENO <- (b$FLASER == 2 | b$PLASER == 2) + 1
b


As you can see,

row 5:

b$FLASER is NA, b$PLASER == 2 evaluates to TRUE -> b$PHENO is TRUE

row 10:

b$FLASER == 2 evaluates to TRUE, b$PLASER is NA -> b$PHENO is TRUE


So the code is not broken by NA's

Hope this helps,

Rui Barradas

On Wed, Apr 29, 2020 at 4:10 PM Rui Barradas <ruipbarra...@sapo.pt> wrote:

Hello,

Here is another way. The condition returns FALSE/TRUE or 0/1. Add 1 to
get the expected result.
It has the advantage of being faster.

b$PHENO <- (b$FLASER == 2 | b$PLASER == 2) + 1L


Hope this helps,

Rui Barradas

Às 20:42 de 29/04/20, Ana Marija escreveu:
Thanks, I did this:
b$PHENO<- ifelse(b$FLASER ==2 | b$PLASER ==2, 2, 1)

On Wed, Apr 29, 2020 at 2:36 PM Ivan Krylov <krylov.r...@gmail.com> wrote:

On Wed, 29 Apr 2020 14:19:18 -0500
Ana Marija <sokovic.anamar...@gmail.com> wrote:

My conditions for creating a new column PHENO would be this:

if FLASER or PLASER =2 then PHENO=2
otherwise PHENO=1

On Wed, 29 Apr 2020 15:30:45 -0400
"Patrick (Malone Quantitative)" <mal...@malonequantitative.com> wrote:

If you don't mind using tidyverse, you can do this easily with
if_else.

...and if you want to stay with base R, you can use the ifelse
function.

--
Best regards,
Ivan

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