counting characters starting point

Hello,

Try

seq1 <- 'PQRTUWXY'
seq2 <- 'AQSDSSDHRS'
seq3 <- 'EEZYJKFFBHO' 

ref1 <- 'U'
ref2 <- 'S'
ref3 <- 'Y'

fun <- function(seq, chr){
	f <- function(x, seq, chr){
		pos <- regexpr(x, seq)
		if(pos < 0)
			99
		else
			as.integer(pos - regexpr(chr, seq))
	}
	sapply(LETTERS, f, seq, chr)
}

rbind(
	fun(seq1, ref1),
	fun(seq2, ref2),
	fun(seq3, ref3)
)

Hope this helps,

Rui Barradas


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