r - The condition has length > 1 and only the first element will be used -

i have dataframe, trip:

> head(trip.mutations)   ref.y variant.y 1 t     c  2 g     c  3     c   4 t     c  5 c      6 g      

i want add third column, muttype, follows these rules:

for (i in 1:nrow(trip)) {    if(trip$ref.y=='g' & trip$variant.y=='t'|trip$ref.y=='c' & trip$variant.y=='a') {       trip[i, 'muttype'] <- "g:c t:a"    }    else if(trip$ref.y=='g' & trip$variant.y=='c'|trip$ref.y=='c' & trip$variant.y=='g') {       trip[i, 'muttype'] <- "g:c c:g"    }    else if(trip$ref.y=='g' & trip$variant.y=='a'|trip$ref.y=='c' & trip$variant.y=='t') {       trip[i, 'muttype'] <- "g:c a:t"    }    else if(trip$ref.y=='a' & trip$variant.y=='t'|trip$ref.y=='t' & trip$variant.y=='a') {       trip[i, 'muttype'] <- "a:t t:a"    }    else if(trip$ref.y=='a' & trip$variant.y=='g'|trip$ref.y=='t' & trip$variant.y=='c') {       trip[i, 'muttype'] <- "a:t g:c"    }    else if(trip$ref.y=='a' & trip$variant.y=='c'|trip$ref.y=='t' & trip$variant.y=='g') {       trip[i, 'muttype'] <- "a:t c:g"    } } 

but error:

warning messages: 1: in if (trip$ref.y == "g" & trip$variant.y == "t" | trip$ref.y ==  ... :   condition has length > 1 , first element used 

i don't think logical statements should producing vectors, maybe i'm missing something. trip$muttype should end looking this:

muttype a:t g:c g:c c:g a:t c:g a:t g:c g:c t:a g:c a:t 

can spot what's wrong here? need || instead of | perhaps?

you error because if can evaluate logical vector of length 1.

maybe miss difference between & (|) , && (||). shorter version works element-wise , longer version uses first element of each vector, e.g.:

c(true, true) & c(true, false) # [1] true false  # c(true, true) && c(true, false) [1] true 

you don't need if statement @ all:

mut1 <- trip$ref.y=='g' & trip$variant.y=='t'|trip$ref.y=='c' & trip$variant.y=='a' trip[mut1, "muttype"] <- "g:c t:a"