words.pos {seqinr} | R Documentation |
word.pos
searches all the occurences of the motif pattern
within the sequence text
and returns their positions. This
function is based on regexp
allowing thus for complex motif searches.
words.pos(pattern, text, extended = TRUE, perl = FALSE)
pattern |
character string containing a regular expression to be matched in the given character vector. |
text |
a character vector where matches are sought. |
extended |
if `TRUE', extended regular expression matching is used, and if `FALSE' basic regular expressions are used. |
perl |
logical. Should perl-compatible regexps be used if available? Has priority over `extended' |
The regular expressions used are those specified by POSIX 1003.2,
either extended or basic, depending on the value of the `extended'
argument, unless `perl = TRUE' when they are those of PCRE,
ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/.
`perl=TRUE' will only be available if R was compiled against
PCRE: this is detected at configure time. All Unix and Windows
system should have it.
a vector of positions for which the motif pattern
was
found in the sequence text
.
J.R. Lobry
citation("seqinr")
myseq <- "tatagaga" words.pos("t", myseq) # Should be 1 3 words.pos("tag", myseq) # Should be 3 words.pos("ga", myseq) # Should be 5 7 # How to specify ambiguous base ? Look for YpR motifs by words.pos("[ct][ag]", myseq) # Should be 1 3