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

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You get the error because if can only evaluate a logical vector of length 1.

Maybe you miss the difference between & (|) and && (||). The shorter version works element-wise and the longer version uses only the 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 the if statement at all:

mut1 <- trip$Ref.y=='G' & trip$Variant.y=='T'|trip$Ref.y=='C' & trip$Variant.y=='A'
trip[mut1, "mutType"] <- "G:C to T:A"

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