n.obs.pat: a function returning the number of observed motifs in a...

In muhligs/Regmex: Motif discovery in ranked lists of sequences

Usage

n.obs.pat(pattern, seq, overlap = TRUE)

Arguments

pattern
seq
overlap

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (pattern, seq, overlap = TRUE) 
{
    if (!overlap) {
        nobs <- gregexpr(pattern, seq)[[1]]
        if (nobs[1] == -1) {
            return(0)
        }
        else return(length(nobs))
    }
    seq = seq
    k <- regexpr(pattern, seq)
    count = 0
    while (k[1] != -1) {
        seq <- substring(seq, k[1] + 1, nchar(seq))
        k <- regexpr(pattern, seq)
        count = count + 1
    }
    return(count)
  }

muhligs/Regmex documentation built on Sept. 5, 2020, 1:11 a.m.