```
searchPattern <-function (dict0, BSgenomeName, outfile = "")
{
if (missing(dict0) || class(dict0) != "DNAStringSet") {
stop("dictO is required as a DNAStringSet object!")
}
if (missing(BSgenomeName) || class(BSgenomeName) != "BSgenome")
{
stop("BSgenomeName is required as a BSgenome object!")
}
if (file.exists(outfile)) {
stop("outfile specified as ", outfile, " already exists! Please rename the outfile!")
}
seqnames <- seqnames(BSgenomeName)
seqnames_in1string <- paste(seqnames, collapse = ", ")
append <- FALSE
for (seqname in seqnames) {
subject <- BSgenomeName[[seqname]]
cat(">>> Finding all hits in sequences", seqname, "...\n")
for (i in seq_len(length(dict0))) {
patternID <- names(dict0)[i]
if (length(patternID) < 1) {
patternID = paste("pattern", i, sep = "")
}
pattern <- dict0[[i]]
plus_matches <- matchPattern(pattern, subject, fixed = FALSE)
if (length(plus_matches)>0)
{
names(plus_matches) <- rep.int(paste(patternID, "+",sep="."), length(plus_matches))
writeHits(seqname, plus_matches, "+", file = outfile, append = append)
append <- TRUE
}
rcpattern <- reverseComplement(pattern)
if (rcpattern != pattern) {
minus_matches <- matchPattern(rcpattern, subject,fixed = FALSE)
if (length(minus_matches)>0)
{
names(minus_matches) <- rep.int(paste(patternID,"-", sep="."), length(minus_matches))
writeHits(seqname, minus_matches, "-", file = outfile, append = append)
append <- TRUE
}
}
}
cat(">>> DONE searching\n")
}
}
```

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