How to omit NA values while pasting numerous column values together?

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You could try na.omit() to omit the values, then paste. Also, you could use toString(), as it is the equivalent of paste(..., collapse = ", ").

apply(dd2, 1, function(x) toString(na.omit(x)))
# [1] "A, AK2, PPT"      "B, HFM1, PPT"     "C, TRR"          
# [4] "D, TRR, RTT, GGT" "E, RTT"

If you have specific columns you are using then

apply(dd2[, cols], 1, function(x) toString(na.omit(x)))

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